The funny business in Amazon's pricing is their Egress Bandwidth, everything is rational.
You're looking at the pricing from a 'cost plus' perspective which is not generally how things are priced.
AWS core use case is IT departments being able to offload all of their infra.
It's a massive, massive advantage. It's so, so much easier and more flexible to use AWS that there is no comparison. It's a 'no brainer' from a cost perspective, which is why, cost usually isn't a barrier with AWS.
Cost only becomes a primary issue when the margin of AWS services is reflected in the cost of the product itself, i.e. when you are hosting a lot of content.
So if you are Phizer, and your IT department uses AWS, the cost is irrelevant.
If you are Dropbox, selling storage for $X/Gigabyte, and your competitors are reducing their prices and you're giving all of your margin to AWS, then you have to do something, i.e. 'make your own infra'.
Is that still cheaper? When you have 30+ very well-paid dedicated DevOps specialists? Maybe it is, I am just skeptical while looking at it as an outsider and without solid data.
And yeah I agree about the "some services are super low cost so you get hooked" thing. Always been my impression of Amazon: they look for what they can apply scale savings on (usually object storage, it seems) and make it cheap and then over-charge for almost everything else.