I really liked this post by an Andrewsullivan.com reader:
http://andrewsullivan.theatlantic.com/the_daily_dish/2009/11/popular-sovereignty-and-the-gays.html "Equal rights and the consent of the governed are the principles that make self-government intelligible in the first place. Without them, of course, there are no real limits to what majorities can enact, including doing away with democratic rule."
If voting and democratic government are not ends in themselves, but only (fallible) ways to achieve the more fundamental good of equal rights for all; then it makes sense to put limits on what a powerful majority can do to a minority, even via the democratically-expressed popular will.
But on the other hand I'm not entirely confident that we can accurately enshrine eternal principles, which, once proclaimed and affirmed, must not be afterwards altered by the votes of living citizens. There's no way to fix a screw-up.
The bill of rights and the constitutional amendment process seem a makeshift compromise at best.