Those FSX clouds sadly are fps hogs when using any kind of super-sampling AA. That's by design and even the strongest cards struggle there, more or less.
You can test this when altering the AA mode and then starting FSX with a cloudy setup. The impact should be less severe then.
As a downside, the image quality then goes down a bit too, but this depends on personal preferences of course.

When using an ATI card, the shader 3.0 mod can help you with cloud performance. Just google it, this should lead the way to some Avsim resource where you can download it.