Why doesn't Neil Patrick Harris get top billing?

Ted and Robin were the main characters, so those actors would get top billing. He was the best character, best actor and became the biggest star because of the show, but contracts were probably signed.

Mainly, because he wasn't the main character. That was Ted, as the story was told from his perspective, not Barney's.

You could argue that NPH wasn't the biggest star when the show started either. It was kind of his break out role, whereas Alyson Hannigan was already known from Buffy and The American Pie movies amongst other things.