At the risk of sounding like I'm patting myself on the back, I'm a guy with complementary/similar problems.
Re sexism, I don't always wanna "wear the pants" and find that many women are every bit as sexist as men, having fully embraced stereotypical gender roles, inside and outside of the bedroom, even those who try to be or would like to think of themselves as liberated. Of course, they are largely casualties of societal pressures/conditioning. On the other side of the coin are those who struggle against this so fiercely that they confuse independence with being noncommittal, thinking they can't be independent and in a relationship.
Re intelligence, seems to me there are two camps of atheists (in general, not just women). The first are the f***off camp, who seem to be just generally anti-everything, usually identifying politically as libertarians, having a visceral reaction to authority in general. To put it nicely, these are not generally girls with whom I can debate philosophy.
The second camp, the freethinking/skeptical contingent have come to their godfree state through a rational growth process and these I find damned sexy. Problem is, I think I intimidate some women who identify as intelligent, perhaps (and this is speculative on my part) because they're not accustomed to dating men who challenge them intellectually and find this unsettling, since they can't adopt the familiar role of the "smart one" in the relationship. I fear this sounds arrogant, but I can imagine feeling some insecurity if I met someone who I discovered may be "smarter" (whatever that means) than me.
EDIT: Woah, just looked at your profile and saw that you're in UT. Poor thing. Best of luck. Is moving an option? ;)
What is interesting is the dualism in gender connection; in your case, regarding men that bore you; yet, are atheist. For women, I meet urban, up-to-speed conscious women aren't afraid to let their hair down. I believe the proclivity of men are anti-social in the halls of the intelligentsia; however, with women, the reverse exists.
Environmental exposure plays a tremendous part in how one corresponds to their social spectrum.