The polytheists of Arabs at the time of Prophet Muhammad were not atheists. They recognized one true God (i.e., Allah) who created the universe, the earth and the heavens. In this way, their belief system was better than today’s atheists who do not belief in a God creating the universe.
A group of philosophers -like Aristotle- think that the universe was there since eternal time, and was existing simultaneously with the creator (which he would call the prime cause, or the unmoved mover). According to them, God does not do things according to divine will, and He never answers those who supplicate to Him, nor He knows the details of things, rather He knows only abstract generalities.
It is therefore utmost importance to understand that, a) the majority of those who are not monotheist are not atheists either, and b) that this majority of polytheists do not deny a true one God, but associate with this One God partners who share with this God some of the qualities and attributes that belong to God.
Given this understanding, we can recognize that Christians were polytheists when they gave Jesus attributes of God. Similarly, the first form of polytheism in the human history emerged from attributing super power to dead people thinking that they have power to answer calls.
One of the contemporary forms of associating partners with one true God today is taking a dictator leader as God and taking this dictators commands as divine orders. If God said something and this leader said something else, the polytheists today will obey the leader and disobey God. Often this leader will keep an army of pet religious scholars who will issue religious verdicts legitimizing the command of this leader as divine instructions. This leader will throw into jail (or execute) any true enlightened scholars who tries to unveil the ugly face of the dictator and his/her pet scholars.
History is full of this kind of scenario. Almost all prophets had to deal with this kind of leaders and his pets. Prophet Moses had to deal with Pharaoh and his ministers and magicians. Pharaoh and all his armies were drowned in sea, and Moses remains a respected figure in history. It is then a choice that rational man needs to take today. Do you want to remain a pet and a worshiper of a human dictator for the sake of some temporary comfort but be cursed by the next generations, or do you endure some wordly temporary pain for an enternal pleasure and the good reputation for future generations?