It's not that yuri isn't about lesbians. More like, every people has a different view of yuri in Japan. Some think it's just about strong friendship, some think that's about romance between girls regardless of their sexuality (the infamous "I'm not gay, but I love you), and some think it's about lesbians stories.
It's a niche genre, so it makes sense that they'll try to appeal to everyone.
Also, the word "lesbian" carries a political view, something that otakus usually avoid.
There's also that fact that the guy responsible by SonoHana series said. They wanted to make girls loving girls looks like the most natural thing in the world, so using a word to make it something "different" isn't a good idea. Yuri isn't about political agenda, it's about entertainment, and sometime escapism. That's why a lot of works avoid themes like homophoby. I think even their lesbians readers want to read something to escape that.
Assuming that every reason why the genre is so subtle is because the public are homophobe is wrong.
I myself like it subtle. I think it's nice when they make it clear that a character like girls without having to make her yell: "Look how gay I am!". That looks as silly as a straight character showing how het they are.
The thing about Nanoha, for example, is that it was never supposed to be a yuri ship to begin with. The writers clearly tried to force Nanoha x Yuuno for a long time. It just become a subtexty thing because fans took that way...and the seiyuu actually helped them.
If the fans had a different reaction, I'm sure Nanoha would be married with Yuuno in Strikers.
Also, the assumption that yaoi is more serious than yuri is wrong. I saw people complaing about every yaoi work was about a guy that would say they were not gay, but they loved that one guy only. That when it was not about a guy falling in love with the guy that raped him.
The fact is, something like this story would never be yaoi, because yaoi isn't about emotional bonds, but about fetishizing gay sex to female readers.
Anyway, I'm kinda tired of people complaining about the way theses slice of life works. Comedy stories rarely have serious romance, even with het couples. And when they do, they get boring, like it happened with Working!.
Also, we don't know if these stories are meant to be yuri or not, because we can't enter the authors mind. But keep in mind that most of theses authors made yuri or yaoi in the past, so they're okay with it. Also, forget about how other people will see it and just enjoy it by how you interpret it.
These are not political stories. They're not meant to be a view of social issues, but a fun read.