It's a theory that Solar Wind caused Mars to lose it's atmosphere.
Apparently Earth has lost some of it's atmosphere for the same reason:
"Solar wind blows some of Earth's atmosphere into space."
http://science.nasa.gov/science-news/science-at-nasa/1998/ast08dec98_1/
I've read (or seen on a program somewhere?) that if we're ever perfectly aligned with a flare of the right magnitude, that the results would be devastating. I can't quite remember why though. I think that it was for more reasons than the loss of atmosphere.... Massive electronics and power grid loss maybe ((Edit) as in Danno's post)?
Now if we lost
all of our atmosphere........
Plus, our magnetic field is due for a massive shift soon. Not quite sure how that might change things.