The trouble is, it's easy to give one class new things that the other doesn't get, making them unequal again. Making marriage equal ensures everyone acts fairly when modifying the legal institution of marriage.
edit: Since HN won't let me reply to bluntly_said --
Trouble is, the fight to move those rights to civil unions and properly separate church and state is a decades-longer fight. I would like to be able to get those essential legal protections within my lifetime. We can finish the job in a few years when marriage equality is universal.