Equal protection under the law means that all citizens must be treated equally. Doesn't matter with race, gender, religion, handicap, sexual orientation, etc.

By placing limits on who you can marry (you can only marry people of opposite gender) you are not treating all citizens equally. The only time government can not treat citizens equally is when it is serves a governmental interest and they way they are achieving that government interest is an enumerated power in the constitution.

Thus the government can choose not to treat its citizens as equal if it furthers some other government interest. The government can discriminate in marriage by only allowing opposite gender marriage because it makes society better in some way, and this better way further some governmental interest.

All rights and powers are subject to balance tests. With equal protection under the law (14th amendment and to limited extent 5th amendment due to due process clause of 5th amendment) Discrimination must pass "scrutiny," usually the scrutiny is the lowest which is called rational basis, but there is an intermediate scrutiny, and the highest called strict scrutiny.

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Pretty much the court threw out DOMA for the rational on only opposite gender couple marriage is bullocks.