I’m intending that a ship would need to roll a 6 to hit, but a Musketeer or a Marine wouldn’t need to roll a 6 to hit the fort. Is that clear from the ability text as it is currently worded?
You should put the text about the Marine and Musketeer first, then. Even though the other part does say “ships”, having it listed first does kind of imply that the same goes for the others too.
Either way, things are a bit nebulous for the Musketeer, because it’s technically adding a cannon to the ship rather than being its own separate thing. It could be argued that they still need to roll a 6 to hit, but would eliminate two flags when they did.
ADDED:
Actually, a more clear alternative would be to call the distinction out directly, maybe something like this:
“Ships can only eliminate this fort’s flags on a cannon roll of 6. Marines and Musketeers can hit this fort normally, and eliminate up to two flags when they do.”