Mesalamine isn’t usually used to treat pouchitis, but it’s common for cuffitis. Your doc might be considering the possibility that you have/had both, and trying mesalamine to reduce the possibility of multiple conditions confusing things. Mesalamine doesn’t work very fast, though, so it’s less satisfying than antibiotics. It certainly takes longer than four days to work, when it works at all. And you might not have cuffitis.
The flu makes everything trickier, since many of us have pouches that behave poorly when we are sick in other ways. You might just have a pouch that’s pissed off about the flu.