one of the things that archaeologists point out is that there was a "destruction horizon" that set in previous to the arab invasions. what that means is that cities were destroyed on a large scale, and never rebuilt - the abandonment of the region by rome (which may have been shortlived in initial intent) is something you can see in the archaeology of what happened. and, so they talk about how the character of the region changed from an advanced, urban society into an agricultural society. and, then the arabs moved in - which makes sense, because they were migratory, and would have walked into open grazing land.
there were diseases that would have also contributed to the depopulation.
and, you could even suggest that this was essentially the apocalypse, in the sense that the prophets had some grasp of geopolitics. to be clear - i'm not suggesting that god destroyed the earth, and islam is the antichrist (even if it's tempting). i'm just pointing out that the prophets were ranting and raving in the context of existing geopolitical facts, and that this kind of massively destructive war between europe and iran, that would leave the levant demolished, was predictable as far back as biblical times. the fact that they saw it coming doesn't mean that prophesy was actualized so much as it demonstrates it was obvious.
that dark age, like others that occurred after similar destruction horizons (like the late bronze age collapse) takes a few centuries to lift. and, when it does, islam is this formed thing, with a set of myths built up around it - almost all of which are dated to centuries after the fact. but, you try to question that in the region, and you lose your head - and that's been true for over a thousand years. so, the myth, as it emerges from a dark age and a civilization collapse that preceded it, just perpetuates itself.
you can believe that mohummad existed if you want. i don't really care, so long as you don't try to legislate your morals on me. and, i'm able to separate these things, even if i see the causality.
but, there's really no actual good reason to, and the correct scientific answer is that he's equivalent to a fictional character, even if he did.