does John like being with Rodney because Rodney's obliviousness excuses John from certain social niceties? In a way, John can be friends with Rodney easily and lazily because social interaction with Rodney takes much less effort than it would with anyone else.
Oh, I don't think John has to be perfect and follow all of Miss Manners rules around Rodney. I think John would love being able to speak his mind on a number of things with Rodney, like saying how he really feels about certain people things. Or enjoys egging Rodney on when he starts acting really badly, because he finds people's reaction to Rodney's personality amusing, but that said, I don't think it gives him carte blache to act in any way he feels. The main things I've seen him do to really hurt Rodney come down to trust and loyalty. Rodney is an intensely loyal person, so seeing John do things like stick up with Col. Ellis (over Elizabeth and himself) is something that would really hurt Rodney. And while I think Rodney would respect John's right to make his own decisions (even if he thinks John is wrong, and an idiot for thinking so) the fact that John never stops to explain to Rodney why he sides with Ellis, but instead makes jokes about it... that's insensitive to a level that's hurtful to Rodney. Rodney may be insensitive in general, but I think he really tries when it comes to the people he cares about, and if he does trip up, he'll bend over backwards to try and fix it. Look at how he acts around Jeannie? The kind of abuse he just takes from her, because she says he needs to make it up to her.
The trust thing is a bit more complicated, I think John still holds Duranda against Rodney. To Rodney his intelligence is his most important characteristic, it's what he draws on as most important about himself and it's his main weapon and tool in this new and dangerous galaxy. So when John tells/shows Rodney that he doesn't trust him on intellectual matters it hits Rodney where it hurts the most. Especially since John (and the others, but John is often the one saying it) seems to demand so much from Rodney's intelligence, often the impossible. The perfect example of this being the season 4 opening eps, where we see John constantly stopping Rodney, who doesn't have the time to stop, to get him to explain what is going on, like he has to constantly watch Rodney to make sure he's doing the right thing and not getting them into more trouble. Or when the shield started to collapse he demanded that Rodney slow it down so they could save the people out there (which was impossible, making it feel like it was Rodney's fault for not being able to pull something impossible off this time), or even when he was adding the hyperdrive to the jumper, and I think it was John who asked if it was going to work and Rodney started to say, that he thinks it will, but he can't guarantee that it will, but he was cut off and made to say just a yes or no, so that if anything did go wrong, everything would be back on Rodney, despite the fact that he tried to explain that he can't be held responsible. John seems to push Rodney a lot when it comes to his intelligence, sometimes it's pushing him further, but sometimes it's pushing Rodney down, and John never seems to do the pushing in a kind way.

I've seen several people mention (here and elsewhere) that a lot of John's character development has been due to JF's acting, which boggles me. I think JF is a pretty mediocre actor,
I tend to be with you on JF not being a stellar actor (god, I can't enjoy Doppelganger, no matter how much other fangirls squee over the slashiness, because I just can't get past JFs horrible acting in that ep :S), but I can still see people attributing John's development to him. Not least because from what I've heard, JF is the one in there pestering the writers to give John the kind of episodes that allow character development.