How can you do that when it is very explicitly stated that Tooru loves Kobayashi despite being the a girl as well.
For the same reason that some people will try to ship yaoi pairings and deny the canon legitimacy of heterosexual relationships - people see what they want to see. It's just that for once, something yuri has enough mainstream success (that is, it's not something people watch explicitly because it's yaoi/yuri) that you have the straight-shippers having a short-circuit.
It seems like some people think it needs to be sexual for it to count as yuri. And for the record, I haven't watched the show yet, planning to do so after it has ended since I missed the start. But from all the fan art I've gotten the grist of a few things that has happened.