the real question is why we should allow a minority group to block the voice of the majority in a democracy.
I suppose another good question is whether or not the concept of a president is still a good idea in this day and age. As it stands, a filibuster is often the only thing preventing sitting presidents from waging totalitarian and unopposed rule.
Also, the whole "majority rule" is also terribly flawed... as is the problem of Direct Democracy, or as some have termed it, "Mob Rule." The adage Democracy is two wolves and a lamb voting on what to eat for dinner rings true in this instance.
But your point that its problematic is certainly substantiated. I'm just not sure that the alternative is better.
"Reason obeys itself; and ignorance submits to whatever is dictated to it" -- Thomas Paine