Hmm, I'd say the biggest reason that male protagonists are used in shounen is mainly because of the target audience, just like the protagonist in a shoujo is usually a female. I don't know about anybody else, but when I was growing up, I had a very hard time getting into anything that had a female protagonist simply because I couldn't relate to one. Growing up I was a very narrow spectrum reader - a habit I've hopefully gotten over - and unfortunately I believe a lot of youth today are as well. There are obvious exceptions to this, such as Claymore. But at the same time in Claymore, I think it's more so because of the shounen-esque plot rather than the characters themselves which makes it a good story.
In addition to that, I think a lot of male mangakas make their protagonists male simply because it's a lot easier for them. I remember reading in an interview that masashi kishimoto could not make a convincing female character and had to get help from a friend in order to create Sakura. It's usually easier to create a character that's similar to you in which you can pour your own experiences into.
I would say gender is a lot less important in plot driven stories rather than character driven stories on the basis of relating with your audience. But then again, at the same time, there are character driven stories with female protagonists that I have had no trouble relating to. I read an amateur comic called "Gatekeepers" who had a very relatable protagonist and made the story interesting to read.
So I guess what I'm saying is gender doesn't matter as much as you'd think. What really matters is your characters, your plot, and what you do with them. A good manga will be popular. That is all there is to it (unless, of course, you don't get exposure, don't get into the right avenues, keep your comic small... but let's just ignore that).