First off, I will say that I am for gay marriage.
One of the reasons a large number of people are against the ruling is because of the way it was decided. I, too, find the process through which the ruling was made in-just.
The job of the Supreme Court is to judge a law and see if, by the Constitution, a law is legal. Anything outside the Constitution is decided by the states. Many states were already making gay marriage legal. Since there is no law in the Constitution regarding gay marriage, the law was supposed to be made individually by each state. The Supreme Court overrode the States' right to chose whether gay marriage is legal. That is one big concern. Furthermore, since the decision was made by the supreme court, which is picked by the President, many felt that the decision was biased and not properly though through.
Again, let me state that I believe that gays should have the right to marry. However, the method with which the ruling was made was objectively unconstitutional.
TL;DR States are supposed to have the right to decide on gay marriage, meaning that the method used for the ruling was unconstitutional.