Money presumably. It's a lot easier to get a good design for your site or app if you have a decent amount of money to pay professional designers. Which most open source foundations and charitable organisations don't have.
Edit: Though I guess it could also be because a lot of alternative software and services are created by people with a 'hacker' or 'programmer' mindset, where very little attention is paid to the UX and everything is focused on the features/tech stack. They're the same people who seem to think IRC, email lists and newsgroups have decent UI.
Edit: Though I guess it could also be because a lot of alternative software and services are created by people with a 'hacker' or 'programmer' mindset, where very little attention is paid to the UX and everything is focused on the features/tech stack. They're the same people who seem to think IRC, email lists and newsgroups have decent UI.