JRPG heroes are presented like that because they have the ability to grow over the course of the game, much like the characters of a book or movie might. Having a hard badass for a main character leaves no room for growth in the story of a JRPG, unless he grows to be more sociable towards the other characters, but that's not nearly as interesting or relatable as a weak, wimpy person becoming someone who can stand up for themselves when it matters. And the reason why this is done is indeed because Japanese men are very timid, so these characters who can and do change who they are are meant to inspire confidence. And the reason why they get the girl is because of that as well. It's a "you can become the person you want to be" sort of thing. Guys here in America don't always have these confidence issues, so it makes less sense to them, but in a game, just like in a movie or a book, it's satisfying to see a weak person become strong over the course of the story.