Okay, that's the side of the fandom I don't see, and I understand your frustration. But it definitely isn't all John/Rodney fans, or even the majority.

A month or two ago there was a huge blow up over a fic in which Keller was apparently killed off just so that Rodney and John could be together (I don't know exactly how, because I couldn't bear to read the fic). Most of the people who were outraged were John/Rodney fans. And yes, they commented publicly, and yes, it created a (unspoken, but real) schism among John/Rodney fans.

I don't know if it affected the amount of public Keller-bashing or not. It's hard for me to tell because my flist is skewed towards people who oppose bashing. So perhaps it's wrong of me to hang out in my safe little corner of fandom, but fandom is my happy place, and that's how I cope.

ETA: The more I think about this, the more I realize I have no idea if I'm in the majority or the minority. Ack! I'm not trying to defend John/Rodney fans as a whole, or to say the bashing doesn't exist. Not at all! What I'm trying to say is that you're not alone, and that there are John/Rodney OTPers who are frustrated with exactly the same thing. *hugs*