I'm beginning to think my WIP has two protagonists. But, I've read that publishers don't accept books with two protagonists. Who is the protagonist in Game of Thrones?
I can think of books with multiple protagonists, particularly in SF/F. I think what you read isn't reliable.
I don't see a problem in you doing it but you are going to have to write it like two books then smash them together in parts where they mesh. Think of the movie Starship Troopers, followed threes main characters from high school, deciding their future, military training, and war. You can do it.
Where are you getting your information from? Lots of published books have more than one protagonist. I wouldn't worry about it.
I think if you do it well, you can break any of the standard rules. Sticking to what you think publishers will go for could lead to something a lot less interesting.
A lot of books have two or more main characters. A song of Ice and Fire, Lord of the Rings to name two rather well known books with them. As long as you balance it well and the writing is great I cant see why a publisher wouldn't take your book because of it.