I think you'll find that when it comes to defense, bumping up from light to medium, medium to heavy, and heavy to assault does not provide any significant defensive boosts. I assume it's because the devs would rather have mech combat be more skill related than feel like rewarding skill with easy-mode mechs.
The atlas does seem more vulnerable than others though. I'd have to say the placement of the head is the key factor right now. LRMs (not clan ones) travel in a straight line down to the target. Since atlases can't move fast, these missiles often hit just the head, shoulder, or arm. They're effectively gauss rifles sometimes.
The other problem is more social. Everyone that sees an assault almost immediately turns their attention to it. It's the biggest and (theoretically) most threatening target, so they get dog piled very quickly. On servers with more than 16 people, this pretty much turns assaults into jelly.
Finally, I noticed the atlas prime's srm6 is missing from the leg. I'm under the impression not all of the weapon spots have been sorted out on mechs, though I doubt a simple srm6 is going to make the difference with atlas. Still, once those are sorted out, we may see more firepower for assault mechs, which may or may not improve their situation.