It is possible for GI Joe and Cobra to take on some normal size transformers... but there's a lot of them and it's not easy, especially the skilled ones, the bigger ones like the Combiners are incredibly tough, and the biggest two are... well...
(Trypticon/Metroplex, respectively, the biggest two normal transformers)
Throw in that they have rather high tech themselves, and DTM's right, either faction could wipe GI Earth if it desired to.
Now, GI Joe or Cobra can make a difference when there's a limited contingent of Transformers on planet, especially when they merely need to tip the balance between the two TF factions, but there's more Cybertronians than the number that come to Earth at any time.
If GI Joe/Cobra try and bulk out their forces, it's with largely useless grunts. If Cybertronians do, it's with a variety of giant robots.
Exactly. *Some* GI Joe badasses are so good they can overcome the physical differences to an extent, but they're very few in number.
And on the flip side, the Cybertronians have some super-badasses of their own. If you read the IDW comics, like Sixshot, who's walking destruction, or Arcee, who is a beast in combat and frankly terrifying.
Or Drift (once Decepticon, now Autobot), who is literally a robot ninja.
A better question might be how few transformers do people think it would take to wipe them all out.
Plus yeah there are some monster transformers out there. Metroplex/Tyrpticon/Dinobots/Devastator/I'm sure there's many more I can't think of right now that are either large or can become large.
Though come to think of it, Metroplex is actually so big he can have trouble with small-scale threats getting inside him ^^
In G1, there's something like a half-dozen Combiners per faction. IDW only has a few though, as Combiner tech is new for them.
Oh yea, one fun thing from the recent comics- all of Soundwave's cassettes are killer at ECM. In All Hail Megatron, they'd fire a ton of missiles, and they'd all just miss. Earth targeting simply wasn't good enough to work against Transformer jamming by their ECM experts.