I've never heard of anyone being bothered by a short protagonist. Of all the books I've read, and all the characters in those books, I couldn't tell you whether most were tall, short, average or whatever. Height is usually only mentioned when the character is extra tall or extra short. It's just not important in most cases.
As a short person myself, I probably have a tendency to make my protagonists a bit shorter than other characters, but I honestly don't even mention it for most of them. And if I do mention it, it's typically as a comparison to someone else rather than providing a specific height.
If you're talking about extremely short people, they probably aren't well represented in most genres. Tyrion in Game of Thrones is one of the most well-known. But I wouldn't view that lack of representation as people being bothered by it. If you want to write about a very short protagonist, go for it.