I was browsing the various courses that PADI offer and see ones like the National Geographic Diver, AWARE - Fish Identification, AWARE - Coral Reef, Project AWARE etc.
Now they sound cool and interesting but surely they don't hold any real benefit that you couldn't learn on your own? I mean they don't really hold much except for being aware of oceanic issues or knowing fish?
Learning on your own is encouraged by PADI, the courses are for guidance that goes directly to the stated goals. the pay for PADI is more on the organizational effort of materials and sequencing and the labor of love of the instructor

Are there any benefits that I am missing or is it just a way to make money?
its a way to make the scuba sport thrive. benefits you on your knowledge and in a safe manner (assuming it is done as specified)
so its basic knowledge provided in the materials (you have to expand this knowledge both in content and understanding)
and the VALUE you put on the knowledge provided vs. the cost you were charged for it.