Some people think that Dipper is the protagonist and Mabel is the second main character. But I don't think that's the case for a number of reasons.
1. The plot synopsis of the show describes it as Dipper AND Mabel's adventures in Gravity Falls.
2. Mabel and Dipper are the only 2 characters to appear in every episode and have an important (Not always big) part in the episode.
3. You can't have the show without Mabel or Dipper. Now yes Stan, Soos, Bill, and Wendy are important as well, but when you boil it down to Dipper and Mabel, you can't just take one twin out and expect the same show. It would be totally different.
4. The show is about sibling bonds.
5. Alex Hirsch has said that the show is about the BOTH of them growing up and their bond and differences.