why witness protection? From whom? did they arrest Bob Anderson? Don’t remember what he did exactly. Don’t remember what happened to Adrian Pimento? Don’t remember what happened to hitman of Adrian Pimento?
Jake and Holt go into witness protection from Jimmy Figgis, the crime boss they were trying to take down, because Figgis threatened them. However, it's purely out of convenience that it's just the two of them instead of one or two others along with them.
Bob was indeed arrested for corruption. He was associated with Figgis.
Adrian Pimento remains in hiding.
The hitman was presumably arrested. The FBI agent who hired the hitman was killed by Bob.
I don't think the two cops would immediately go into witness protection after being threatened, but it’s a comedy show, and they had some writing problems after one of cast members got pregnant, so it’s understandable that they would try to shake things up a bit. Not the most brilliant solution, but whatever.