It would seem to me that a larger majority of Muslims / people of Middle Eastern decent are named Muhammad while fewer Christians / people from christian nations are named with direct namesake from Jesus Christ, or people from other religions named directly after their prophet. Is this perception correct, and if so is their a historical reason for it?
Interesting, I always thought about it from the other point of view. If you consider a man to be the best human and a role model to pattern your life on, wouldn't it follow that it should be a very common name? Muslims are supposed to love the prophet Muhammad more than their parents and we know that naming children after people you love is pretty common. With that logic, I think the question should be, why aren't Jesus and Moses more common names?*
*Among Christians and Jews, respectively, of course. They're both relatively common names in the Muslim world (with the Arabic pronunciation, of course).
"Jesús" is very common in Spanish-speaking countries; the English variant "Joshuah" is reasonably well known. Here are a few related threads on the popularity of the names "Muhammad" and/or "Jesus":