This use to bother me a LOT! Now that I've been on T, I don't get stared at much, but when I do, like another poster said, I smile. Or stare back until they look away, usually when you stare back at someone, who's blatantly staring at you, they get uncomfortable and look away. Plus who doesn't like a good staring contest!
What helped me get over this, was dating a girl for 2 years, who was black, me being white. You'd think in California, of all places, people wouldn't be as "shocked", but let me tell you, we got hell. I remember the first time we were out in public, at Universal Studios, I really felt like we were on a stage with thousands of people looking directly at us, it was extremely uncomfortable. After a good 3-4 months, I stopped noticing. I was so used to it, it no longer bothered me. It wasn't my problem, it was THEIRS. Sometimes people just aren't used to seeing something "different" so they stare. Not so much because they think you're a freak, but because it's new to them.
If the GLBT community got angry/sad everytime someone looked at them funny, we'd have to be mad, 24/7, 365 days a year. It's not worth it. As hard as it is, put a smile on your face!