Of course the protagonists are characters with whom readers can generally identify.
But, that isn't the same thing as having 'good morals.'
For instance, I think most readers identified w/ Spider-man because he was a geeky vagrant, not because of his morality.
Also, heros don't have to be role models. Off the top of my head, I don't think Punisher has many redeeming characteristics. Ya, the people he fucks up might deserve their respective ass kickings, but he's no boyscout.
Furthermore, not being a boyscout embellished his commercial viability as a character instead of defeating it.
Thing is though seems peoples moral compass is changing and thus charecters that were popular in the fifties are now not nearly as popular, charecters with a more complex moral compass and personality are becoming mroe popular.
Look how much more appealing Ultimate captian america is in comparision to the mainstream one?
Very true. Post-Watchmen superheroes are more layered and conflicted than their earlier counterparts. In the old days, superheroes were more symbolic too especially in marvel.