What's the difference really? Take Civil Rights for example. The Senate held this up against popular will for at least a decade, and arguably much longer, but we did thankfully finally get the Voting Rights Act and the Civils Right Act, and I would argue that Slavery and Civil Rights were a special case of growing pains that the country had to go through, and not a reason to change the whole structure of government.
I think it's obvious that the authors of the constitution purposely created our government with with built-in dampers against simple majority rule, and I would be very hesitant to remove them.
This is not the case in the Presidential election; the President is supposed to represent all Americans, and yet when campaign season comes around we get maps that look like this: http://www.npr.org/blogs/itsallpolitics/2012/11/01/163632378...
Unless you live in DC. We get disenfranchised there, too.