Why is it legal for a majority to take away the civil rights of a minority?

I've always wondered the same thing. Not just in the context of gay marriage. We live in a democracy that allows the majority to rule, basically. But how do we prevent the majority from disadvantaging the minority? Obviously the minority, in any situation, can't protect itself through popular voting. I guess we have to put our faith in the Supreme Court of the United States to protect whatever minority feels that it is being disadvantaged.