The Primes are defined as being
They are usually portrayed as the first thirteen living beings created by Primus, the creator of the Transformers and their home planet of Cybertron.
I know there are several Transformers creation stories, so this may vary.
Autobots have a different back story
Autobots were the descendants of a line of robots created as consumer goods by the Quintessons on the planet Cybertron. Their bodies were forged by the Plasma Energy Chamber and given intelligence by the mega-computer Vector Sigma in order for the work to be carried out.
So while the Primes, with the exception of the fallen, seem to be on the same side as the Autobots they seem to be a different class of being.
Do the Primes count as Autobots?
There was another question asking if any Autobots had become Decepticons. The Fallen was cited as an example. This would only be true if all Primes were Autobots to begin with.