The choice of the 'right' fonts is very situation-dependent. A font
that's perfect for body copy might be terrible for headlines, and
vice versa. Therefore, the selection of typefaces can not be left to
the operating system, because as you rightly pointed out, it will
always use the same default font. While that default font probably
isn't the worst of all fonts for any situation, it is certainly not
the best.
However, delivering the best experience must be our goal. Therefore,
it is important that the decisions which font to use in which
situation is consciously made. Using a font stack is just a good
practice to ensure that users who can't load webfonts or whatever
still get a font that was picked carefully to suit the situation.
That way, we as designers can still deliver the best possible
experience even to users who for whatever reason can't use our first
font choice.
best, max
@awesomephant