You could argue that Cap help make the Avengers popular but making him a founder is just wrong. He was not in issue #1. By your logic that would make Abraham Lincoln a Founding Father. Also the Hulk leaves after the first issue, which also by your logic means he shouldn't even be in the Avengers.
Well, the thing is, these movies aren't the books. Ant-Man and Wasp should be in the movie, but they're not. Nick Fury shouldn't be in the movie, but he is. Neither should Hawkeye or Black Widow. Also, Iron Man's armor should be bulky and completely gold if we're going by Avengers #1, but I'm pretty sure it won't be.
Hell, they probably could have made an Avengers movie work without Captain America. But they would prefer that he's in it because he is a popular character and he is very much associated with the comic book. It's a change born from creative and (likely) financial considerations - and it's only one of many changes. And I can think of worse things they could have done.
Plus, I've noticed they're basing the new movie more on the recent Ultimates series than the classic Avengers storyline. I'm not the biggest fan of Millar's work, but in that one, Cap was very much a founding member of the team.