So yes, there is actual bitcoin transaction going on if you don't have coinbase account.
...Not that I think it's a bad thing if a bunch of Bitcoin transactions (especially microtransactions) go off the blockchain, I just wanted to point out that off-blockchain transactions weren't inherent to accepting Bitcoin through Coinbase.
For Aaron: Aside from the 53 money transmission agent licenses both are required to hold, but only PayPal actually has.
Having a Bitcoin bank as a middleman is probably the best model for the majority of payments. But Bitcoin's appeal lies in its flexibility. Bitcoin is just a protocol: payments can go through a bank, but they don't have to.
One of the primary advantages of Bitcoin is its decentralization. I realize that Bitcoin != Coinbase and that Bitcoin provides a foundation for many potential services, but if everybody starts using Coinbase/<insert third-party name here> to handle their transactions, what's the difference? Where is the decentralization?