The Future of Us clearly refers to Emma and Josh, our protagonists. The whole plot evolves around the fact that they find their futures, after all, and as the story progresses, we watch them each navigate this discovery in their own ways.
Okay, so that covers the whole future element of the title. But what about the us part? When the story opens, Emma has rebuffed Josh's romantic advances and things are officially awkward between these two life-long friends. So when they first find their futures, it's all about his and hers. But as they quickly realize, what they do in the present matters, impacting not only their individual futures, but their shared one as well—so much so, in fact, that they aren't even friends on Facebook at one point. The future, then, is theirs.
As Emma and Josh both come to understand that the present is what matters more, they begin to repair their relationship in the present. They used to be us and, by the time the book closes, it looks like they're ready to be a duo again. Their rift is repaired, and now all that remains to be seen is what happens now that they're finally together.