Edit (since my original brusqueness earned a downvote):
The flaw is that IE6 cannot resize text sized in pixels. IE7 fixed this with its new zoom feature, but left the old, broken resize method untouched. Every other modern browser can resize pixel-sized text.
I personally prefer sizing text in pixels because browsers handle ems and percents differently. Usually it works out fine, but it's really annoying to futz with fractions of an em because one browser rounded it up while others rounded it down.
Pixels also make the translation from mockups to code a tad easier.