It's pretty common, I'd try not to get too worked up over it. A lot of the ads that are looking for women-only are either guys looking for eye-candy/someone to cook and clean/potential sex partner, or women that wouldn't feel comfortable rooming with men. And really, who can blame them? People have their preferences on who they want to live with. I'd say with the latter, you might try talking to them anyway. If they're trans-friendly at all, and if you seem non-threatening, they might let you stay. And if it's a guy advertising like that then just steer clear anyway unless you're looking for an easy lay with a creep.
Good luck with your search!