Hmmm, I think for Dean it's probably kind of an internal backup of his opinion that the angels don't want Sam using his powers, either. I don't think he actually cares for what they say, but rather knows that Sam would care (at least before he got to MEET angels). That's a nice argument to enforce your own argument, isn't it? "But the angels want it too!"

But I think some things have already changed. Castiel threatened to kill Sam when he used his powers, but neither him or Uriel tried to actually do it after Sam took out Samhain (aside from a little posturing). It looks like an empty threat now.
Also Dean seems to me no longer totally against Sam using his powers (there was no big fight after Samhain), his biggest grievance now looks to be not being included in Sam's plans (with Ruby). In that regard I also think he's not generally against Ruby anymore, because she's a DEMON, but it's because basically she took his place as Sam's most trusted person (or at least it seems so to Dean). He's jealous of her.

But I disagree on him treating Sam like the enemy. That would have meant trying to kill him. Which I'm sure he would have tried had it been any other person with demon powers and not a relative of his he cares about. He's even said so.

Then again I think the show's writers have done a crappy job of portraying someone with Post Traumatic Stress Disorder. I rolled my eyes at the confession beside the car scene as well. That reveal could have been executed so much more subtle and BETTER.