Sometimes it's not about being cheaper but about everything being under your own control.

There are other reasons other than cost that I can think of, physical security and ability to roll your own patches to name but two.

But your company might have security requirements that prevent the use of S3.

For example, if you're a defense contractor that handles FOUO information, you can't just throw that on somebody else's cloud. You have to keep it entirely in-house.

Are you serious? It's definitely possible, and almost simple, to build a limited scale service that is cheaper than S3. S3 has the Amazon footprint behind it, which you can't compete against, but the price is not hard to beat.