Well that is just twisting our words. Saying they don't think of him as a god BECAUSE means exactly that. We provide examples or why it is so. Not just because the fluff tells is that the space marine does not believe that he is a god but also because comparing it straight of with modern day religion doesn't work.
For one thing the Emperor does exist. His miracles are real, the legion of the damned appear out of nowhere when they are needed. People survive orbital bombardment by faith alone and he grants superpowers through visions.
So praying to the Emperor for faith and strenght to fight a bloodthrister can be compared to asking your father to beat up that bully that keeps hitting you. Unlike "God" the Emperor might actually smite the bloodthirsters, (more likely fill you with holy rage and make you do it). That does not make Him a God. That makes Him the most powerful psyker to ever have existed. And that is a example for every space marine. He is a warrior that can fight death by will alone, He is an example above all examples. He is the shield and the protector. But even so, He is a man and even though He posess divine qualities He is not a god.
It makes me think of the quote "technology is magic for the unenlightened" Just as the Emperor appears to be a god for the mortal men, the more enlightened and those closer to Him can see that He is infact a man. A man worthy of prayer, your devotion and faith but still a man.
Taken from lexicanum who in turn took it from an article posted in White Dwarf
0400 - Morning Prayer - Led by the Company Chaplain the Space Marines renew their oaths to the Emperor and the company relics are displayed. This time is also used to give out orders, announcements and other administrative tasks.
Also taken from lexicanum: unknown original source
The precepts of the Imperial Cult, called the Imperial Creed, include the belief that all of humanity must be brought into the Imperium, the abhorrence of aliens, the realization that psykers and mutation among humanity is a dire threat which must be controlled. All of these precepts have their origins with what the Emperor himself preached during the Great Crusade.
While the ordinary citizen believes that the Emperor has always been venerated as an immortal and omnipotent god, this was not always the case. At the beginning of the Emperor's Great Crusade the Imperium functioned very differently. Firstly there was no Ecclesiarchy and the veneration of the Emperor, in the form of a cult known as the Lectitio Divinitatus, was frowned upon. The official Imperial doctrine was that the Emperor was an extremely powerful being, rightful ruler of all mankind, and the perfect image of humanity, but no matter how supreme, still a human being. During the Great Crusade however, many ordinary Imperial citizens found that the light of reason and truth brought by the Emperor was not enough, and they took to worshiping him as a deity1.
The Emperor became an object of general veneration following the Horus Heresy and his internment within the Golden Throne on Terra. Over the following decades many individual Imperial cults sprang up throughout the Imperium, with their central theme being the redemption of humanity through the Emperor's self-sacrifice. After a few hundred years a single cult known as the Ecclesiarchy was formed from the unification of a number of smaller cults, which gradually absorbed the main body of believers. In M32 this cult became the official religion of the Imperium, gaining the title of Adeptus Ministorum. Remaining cults were persecuted and mostly destroyed.
As you can see. Originally (and still among the space marines) He's not worshiped as a God but as a supreme human being to which all shall aspire and obey.
Note on chaplains and the Emperor (yep lexicanum)
Each Chapter has its own unique cult, which is often thousands of years old. As these cults often predate the rise of the Ecclesiarchy and the general worship of the Emperor, the Chapter cults are not simply facets of the common Imperial cult of the Ecclesiarchy. The Ecclesiarchy and its parishioners (its lay followers) worship the Emperor as the most divine god. Although the reverence Space Marines have for the Emperor borders on actual worship, he is supposedly not seen as an actual god by some, but as a brilliant and inspirational man. As in all things, this view of the Emperor's divine status or lack thereof varies from Chapter to Chapter. The Space Marine cults are more ancient than the cult of the Ecclesiarchy, and their specific practices often primitive and barbaric. The chapter's own Primarch is also a major part of the Chapter's specific cult, revered as much as the Emperor.
Within a Chapter's fortress-monastery is the Reclusiam, a large chamber devoted to cult activities, and where the Chapter's holy relics and, sometimes, the body of its Primarch, are housed. The Chaplains lead their sermons from here, and rouse the Marines in their love of the Emperor. The battle barges and ships of the Chapter's fleet also include huge cathedrals in the heart of each ship, allowing the Space Marines to pray while away from the fortress. Chaplains always lead the Space Marines in prayer, but a Chaplain is not always needed for a Marine to pray.
This is all I can find atm (it's 02.00 give me a break) but yeah. Space marines are mostly agnostic, they just love their grandfather