There's always the ability to tweak specifics for your setup that aren't available in many platforms.

IMHO, you shouldn't use a PaaS unless you know how to set your stack up. Essentially, if you don't recognize or have respect for the convenience you're being given (by going through a platform) then you'll potentially make bad decisions down the road. Personally, I prefer to learn how to set it up and scale it myself initially which helps me better understand what to look for in a platform.

Plus, there's something fun about putting all the pieces together and watching your apps come up (especially if you don't normally handle this part of the stack).