Per Justice Scalia:
"Today's opinion has no foundation in American constitutional law, and barely pretends to. The people of Colorado have adopted an entirely reasonable provision which does not even disfavor homosexuals in any substantive sense, but merely denies them preferential treatment. Amendment 2 is designed to prevent piecemeal deterioration of the sexual morality favored by a majority of Coloradans, and is not only an appropriate means to that legitimate end, but a means that Americans have employed before. Striking it down is an act, not of judicial judgment, but of political will. I dissent."
Scalia is just wrong about this. It, quite simply, singles out a politically unpopular group, and tells them that the courts are closed to them for discrimination suits, but not for anyone else.
That is not "Equal Protection."