Pixel font sizes are, in fact, not a CSS misfeature. Careless use is wantonly unhelpful, and browsers that don't implement CSS correctly are Just Plain Wrong, but pixel font sizes are in themselves quite defensible.
Consider font hinting. Many common fonts contain hinting information, designed to make them display better on screen. Unfortunately, not all fonts - even the most common ones - contain this information for all screeen display sizes. Fonts at unhinted sizes are ugly as sin and can be almost illegible. In an ideal world one would avoid these situations, but not all web designers are free to do this (managers being another misfeature of the Real World) and that's where pixel size becomes a Good Thing.
Consider, further, that someone technical like Gamer Joe with their super-high-res screen is probably used to tiny text, and is disproportionately likely to have a proper browser that can overrule anything you set anyway. Aunt Tillie, on the other hand, has Internet Explorer at 1024x768 (like 90% of the internet) and has no idea that users can adjust font sizes. For a commercial site, making things look right for her usually has to be a priority.
And what about those cases where text is meant to be very small? Very small sizes generated automatically are completely unreadable on a fair proportion of browsing setups. Pixel-set Flyspeck 3 may need a magnifying glass, but at least the characters are correctly formed; em-set Flyspeck may not be readable at any resolution.
So as long as developers have to deal with designers and lawyers, it's not a misfeature of CSS. The need for boilerplate might be a misfeature of the world, of course, but that's another story.