Limited character sets: Most free fonts don't include many of the special and extended characters found in (most) commercially available fonts.
Lower quality: Free fonts may not be as well-drawn as commercial fonts. It doesn't mean that there aren't free font authors that do good, even exceptional work, but as a whole, the freebies often don't measure up in overall quality.
Limited formats: The vast majority of free fonts on the Web are in Windows TrueType format. They aren't readily available in Win/Mac PostScript or OpenType or Mac TrueType formats - which is important (or essential) to some folks - and conversions are not always possible.
Free may not really be free: Unfortunately not all download sites are vigilant about making sure that the fonts they offer for download are really free fonts. Commercial fonts are often made available with no indication that they are not free fonts. Some people knowingly place commercial fonts online, sometimes believing that if they bought the font they are free to do whatever they want with it. Not true.

