I don't think it's belief in a God/creator per se that is the problem, it is the widespread belief that ancient scriptures written by scientifically ignorant, superstitious desert dwelling nomads (Hebrew Scriptures, Koran) are literally the inspired word of God that is the problem.
The most primitive and natural religious feeling was worship of the sun and astrological entities. The sun moved and gave light and warmth, the moon changed shape from full to a crescent, the stars and comets moved, etc. These movements were predictable and corresponded to changes in the temperature, length of days, seasons, harvest productivity, etc. All this movement and their apparent affect on earth suggested to the ancients higher power/s that were to be praised/appeased.
This is what is left after stripping away all scripture based ideas of God. Basically, animism.