Gunnerkrigg Court is the best webcomic I ever read (although I'm pretty behind it now).
It does have a female protagonist, but she's not a lesbian. But there's a yuri side-couple, although it takes some time to get to them. There's not focus on het, though.
And it's really, really fun.
Girly is pretty fun and a lot of couples. Although some het couples too (and one yaoi). It's finished, too.
Cucumber Quest does have a male protagonist, but it's really cute and there's one yuri couple (also, his sister gets as much focus as him). And the relationship with the protagonist sister and one of the girl villains who has a crush on her is pretty cute.