political beliefs on campus, and often leaving home for college is the first time a student is seriously and consistently exposed to new ideas. whether it's BYU or Berkeley, there is always a chance that kids will change their minds about a number of issues/ideas when they're at college.
it's sad that your kids are out of the church (or "pretty much" out of the church), but that is a widespread problem for younger generations of Mormons — not just a BYU issue.