I'd like to say it wouldn't matter, but I know for a fact it does. When I went through rush at my school homophobia abounded. In fact, I'm almost certain I didn't get a bid simply because I AM openly gay. That's when I started leading the charge for DLP and that's why I'm currently working to build a chapter: to give gay/bi men a chance to live the fraternity life.
Greek culture is one of the final bastions of traditional sex roles, and while that is changing, it isn't changing rapidly. I think this varies from campus to campus, and of course campuses in bigger cities are bound to have more tolerant Greek organizations. But by and large, as a gay man, I think homophobia does exist.
That doesn't mean it isn't coming to an end though. A lot of the posts I've seen in here have made me realize that the future is bright for gay and lesbian Greeks.