As much as Dean is beta to John's alpha, he's also totally pussy-whipped by Sam.

Or rather, as much as Dean is pussy-whipped by Sam, he's totally beta to John's alpha.

When it comes to making decisions etc, Dean will always succumb to Sam's giant gleaming eyeballs look. See: Skin ("But St Louis is four hours behind us! No fucking way." *giant gleaming eyeballs* *car turns around*), Nightmare ("Promise me you'll follow my lead on this one!" etc).

So I think a good part of what pisses Sam off so much about the remote orders from Daddy-O via text message is that it's pretty much the only time that Dean won't budge to Sam's will. Because no matter how much Sam bitches and whines and threatens and goes all chibi-eyed, if Dad's given orders, Dean will follow them. Sam's bugged by the fact there are orders at all, sure, but he's also bugged by the fact that John's above him in the pecking order. Not that he cares so much that Dean's on the bottom. Well, he feels incensed on Dean's behalf that John orders him around like a good little soldier, but feels no such qualms when it's Sam himself ordering Dean around (because you know, their techniques are different!).

Not that Dean's complaining. I doubt that Dean angsts about being below them in the pecking order, I think he just wants their orders to be the same.