The difference is that there is no federal constitutional right to same sex marriage, but state and federal courts may try to impose it on the other states through other constitutional provisions, including the 14th amendment. These ballot initiatives are wholly applicable within each state because they are based on people-passed laws, not based on constitutional interpretations. So, they would not impact other states.
There is no federal constitutional right to smoke marijuana. And our elected represenatives have voted by the will of the people that this activity is illegal. I think the court ruled correctly in supporting what our duly elected represenatives have legislated.