Is progress in the coop campaign in Portal 2 saved?

Yes, the progress is automatically saved and synced to the Steam Cloud individually - so when you next join a co-op game it will have stored which levels you have completed. This also means that your progress is shared across any computer you play Portal 2 on.

It's worth noting that progress is never saved during a test chamber though, only upon successful completion.

You will be able to pick which level to start at next time you start the game - if you go to the specific chapter you want to play and use the buttons until you've selected the level you want, then go into the assembly machine as usual.