Difference between Outpoint structure returned from Blockchain.info and what is in the Protocol Specification
Why is this different?


Blockchain.info has an API that provides the same data, but not necessarily formatted in the exact same way. When bitcoin nodes talk to each other, they must use the protocol as specified in the link you gave, but the Blockchain.info API is just a utility for getting some data about the contents of the block chain. 


  Is blockchain.info not following the Bitcoin protocol for transactions on their json messages?


In their API, technically, no. I'm sure they have more than a few nodes running, though, which do follow the bitcoin protocol. Their API can call upon these nodes and a few database to return the JSON with the requested info.