oops, I didn't read your question closely enough.
You think dark matter could be proton clouds because you say that only electrons (with negative charge) emit EM waves. It turns out that any accelerating charge emits EM waves, including protons (which have a positive charge).
Don't worry, you weren't totally crazy for thinking this. Indeed, in most situations where both protons and electrons are present, most EM waves come from oscillating electrons. This is because electrons are 2000 times lighter than protons. Think of a bowling ball and a beach ball in the wind, obviously the beach ball will be buffeted (accelerated) more than the bowling ball. Finally, the higher acceleration the charge has, the greater the intensity the emitted EM waves will have.
Notice I haven't explicitly discussed the case of atoms, electrons bound to protons, but, the same idea is roughly applicable (you really need quantum mechanics to understand exactly what's going on).