When it comes down to it, the sole purpose of government is to protect the life, liberty, and property of individuals. This gets interesting, however, when government has multiple levels of jurisdiction and authority, i.e. federal, state, and local. We have two philosophical ways of looking at this when drafting, amending, and interpreting the Constitutions of various levels of government:
1.) Each level of government exists to protect the life, liberty, or property of the people by performing some sort of duty (e.g. a national defense in the case of the federal government). It has the moral responsibility to restrain itself from imposing tyranny on its people, but it has no moral authority to protect the rights of citizens from intermediary levels of government. Under this frame of mind, it would be improper for a government's Constitution to give it the authority to protect the people's rights from intermediary governments. The advantage of this is that lower levels of government essentially always trump higher levels of government, bringing power closer to the people. The disadvantage of this is that even the most basic of individual rights essentially must be fought for at
every single level of government to ensure that the Constitutions of each of those levels prevent them from imposing tyranny. In other words, no higher level of government can force lower levels of government to draft moral Constitutions. As such, small jurisdictions could potentially regress into direct democracy or even a dictatorship; in other words, small towns would be perfectly free to burn witches and gays at the stake, and hang, draw, and quarter anyone caught trying to leave.
2.) Each level of government exists to protect the life, liberty, or property of the people by performing some sort of duty (e.g. a national defense in the case of the federal government). It has the moral responsibility and authority to restrain not only itself, but also intermediary governments, from imposing tyranny on its people. As such, it is perfectly legitimate to draft, amend, or interpret a Constitution in such a way that it forces intermediary governments to respect an enumerated (but
nonexhaustive) list of individual rights. The advantages of this are obvious; as the only real purpose for government is to protect the life, liberty, and property of citizens, it makes sense to me that it should protect them from all threats within reach. Granted, a government that disregards its Constitution (or has an improper Constitution giving it unwarranted power) will be able to trump intermediary governments and impose tyranny, but
that applies equally to situation 1 anyway, since a government gone rampant would impose force regardless!* In other words, giving a government the legitimate power to protect its citizens' rights from intermediary governments (and not just itself) does not pose any additional threat of tyranny from higher level governments, except in the rare case when the higher level recognizes and protects one potential right at the expense of another (e.g. the right to life vs. the right to privacy in the abortion scenario). Even then, the wise solution is to let lower levels decide these conflicts by either:
a.) Not enumerating conflicting rights at all, or preferably,
b.) Explicitly stating that if the government protects conflicting rights, it is up to lower levels to decide how to handle any conflicts that arise.
The only other disadvantage of this is that the dull might interpret an enumeration of rights to be exhaustive, but it is not, unless the Constitution itself is in fact immoral and breaks this view of legitimate authority (by stating that the list is exhaustive). For the record, our own Constitution explicitly states that the enumeration is
not exhaustive in the Ninth Amendment, so this particular disadvantage does not apply to the current Constitution of the United States:
The enumeration in the Constitution, of certain rights, shall not be construed to deny or disparage others retained by the people.
Now, I understand why Ron Paul and others might believe that the incorporation doctrine is flawed (or even phony, as Dr. Paul says); for several reasons, they are actually correct. After all, the Fourteenth Amendment (among others created during the Reconstruction period) was not properly ratified, so it does not really carry the full force of law that
real Amendments do. In addition, you could even argue that the wording itself is somewhat vague and doesn't point to incorporation (although if you did, I must retort that if certain clauses were not meant to enforce the Bill of Rights on the states, what the hell are they actually saying? Meaningless fluff?

). Finally, if we did accept 100% incorporation, state and local laws against libel and slander (among other things) would become unconstitutional, which may not be the most desirable thing in the world.
In light of all of that, I certainly understand (and perhaps agree with) Ron Paul's rejection of interpreting the Constitution (as it stands) in favor of incorporation. Consequently, I also understand the Constitutional basis for the "We the People" Act. However, I do think that Dr. Paul is in the wrong on one thing: Rather than fighting for laws like the "We the People" Act that more explicitly affirm each state's "right" to impose tyranny, shouldn't he be fighting for a more legitimate Constitutional Amendment incorporating the Bill of Rights for the states (perhaps with some exceptions afforded the states to allow for things like slander and libel laws)? In addition, if we cannot interpret the Constitution to protect such things as the right to privacy and consentual sex in the first place, perhaps he should have focused his efforts on drafting Constitutional Amendments affirming such rights? That said, I do admit that the Ninth and Tenth Amendments probably make such "new rights" unnecessary in the federal sense, so they're only really necessary if we're wanting to impose them on states through incorporation.
Obviously, I subscribe to "view 2" of governmental authority as detailed above. I strongly believe in [constitutionally] giving the federal government the authority to protect the people from state-imposed tyranny (and in my book, sodomy laws constitute tyranny). As mentioned above, permitting this does not increase the likelihood of the federal government itself becoming tyrannical. This is one of the very few situations where I have to wonder, "What's Ron Paul trying to achieve here?" In terms of this election, voting for Ron Paul is a no-brainer; he's America's only hope at the moment. That said, I do feel like his judgment is lacking on this particular matter (and that's pretty rare, since his arguments on most issues are very compelling).
*Our own government is such an example, as it infringes upon our rights by outright ignoring its own Constitution. It's too bad the Framers forgot one thing when writing the law of the land: Most laws come in two parts, the "here's the law" part, and the "here's what happens if you break it" part. It's unfortunate there are no clauses promising treason trials (or at least unceremonious dismissals) for legislators that vote for clearly unconstitutional laws (e.g. the PATRIOT Act), executives that enforce them, and judges that fail to strike them down as unconstitutional when given the chance...with leeway given for unclear and iffy violations, e.g. the incorporation doctrine. An enforcement clause would have scared the crap out of government officials and forced them to
*gasp*, actually obey the supreme law of the land.