Interestingly, life was considered just an inherent aspect of the universe up until the 19th century. One aspect of this is the theory of spontaneous generation, the idea that life would arise from inanimate matter spontaneously. For example that dead meat would give rise to maggots, pure water would give rise to algae, etc. Another aspect to this was the theory of vitalism, the theory that living organisms were fundamentally different from inorganic things down to the finest material levels.

Both of these theories were disproven during the early to mid 19th century, shortly before Darwin's theory of evolution was developed. Pasteur performed experiments involving sealed containers of liquid that had been heated to near boiling to kill organisms. His experiments showed fairly conclusively that life doesn't spontaneously arise, it comes from other life.

Meanwhile, in the early 19th century another experiment involved the creation of urea using "inorganic" reagents. Urea is an organic chemical, a product of living organisms and this synthesis basically laid the ground work for the purely mechanistic theory of life. Showing that there was no mysterious difference in the materials that life was made up of than everything else was made of.

Not long after the cellular theory was fleshed out. Cells had been discovered centuries earlier but it wasn't until the 1830s that a model of cells as forming the fundamental building blocks of life was put forward.

All of this came together right around the same time that Darwin's theory of evolution came on the scene, coalescing into the familiar overall theory that exists today: abiogenesis -> cellular life -> humans (via genetic evolution).

Prior to that there were somewhat less satisfying theories of life being an intrinsic property of the universe and there were less sophisticated (and less correct) theories of evolution such as Lamarckism. The answer to the (non-creationist view of the) origin of life itself and the origin of humans was filled with a lot more unknowns than today, which might explain why the form of atheism that would exist later wasn't as prevalent.

(I'm on mobile at the moment and about to board a plane, there's some more detail I'll fill in on the migration from deism to atheism and the science of evolution in the 19th century when I get back online).