Actually the Autobots could fly in the first 3 part episode....then this was ignored for the rest of the series..lol
I think there was a sudden change in continuity when Optimus Prime had to borrow Sideswipe's rocket pack 
The official continuity, after those couple of episodes where they could fly, is that, general rule, Autobots can never fly, aside from ones who end up taking flying alt modes, like Skyfire & Powerglide. The Dinobots, can fly. They were built differently then the other Autobots, so they don't have that limitation. All Decepticons can fly, without question.
However, that's going by race, rather then faction. The Autobots descended from the workerbots that the Quintessons created. While the Decepticons descended from the warriorbots, which could fly. Eventually, they got too smart, & there was an uprising, led mainly by the workers/scientists, though I suspect there may have been warriors involved as well. It seems like most warriorbots, were off the planet(aside from the Omega Sentials), as they usually were sold to warring nations for profit. So I'm not sure how that all works out, if the warriors did indeed fight with the workers, or if they came back to Cybertron at some point. It does seem like, atleast for awhile, the warriors were almost an unknown on the planet in general.
Anyways, my point here is, if an Autobot of race(as it's also established that when a spark comes online, they are born a worker or warrior), joins the Decepticon ranks, he can't fly, unless he has a flying alt mode, or a jet pack. And if a con of race joins the bots, he can fly without exception.
I'm guessing I would be an authority on Transformer lore here, since it's one of my main hobbies, & I'm probably the TF nut on these boards, (though, if you go to the All Spark, there's people with alot more knowledge about G1), so, any questions, ask away.
