In some cases, they're very skinnable and the ugly theme is just the default. Both Winamp and Foobar2000 were extremely popular in the desktop customization community when it was at its height around 2004-2006ish for that reason.

It's also because most of these projects don't have dedicated designers working on them. So you end up with the "designed by developers" aesthetic and let's be honest: we developers generally suck at designing UIs.