It's a cultural thing, which we're loth to admit. We look around and say, "We treat women the same around here", not thinking for a second that maybe that's the problem.
I run the Hackbright Academy, a hacker school for women, and I ask all applicants what compels them to apply to our program. Invariably, part of every story is the idea that they were intimidated out of the field in college or high school by their male peers. Whether or not that's the grand reason for the disparity, it's still something that shouldn't be a reason at all.