Why was Sam Adams written out of this?

I think the best explanation is that this was written as a Broadway show and having a cast large enough to portray the entire Continental Congress would be a little unmanageable as far as stage space (let alone making a buck!), so they abbreviated Congress a little.

You can see little hints of the Broadway origins in Lewis Morris' explanation about why the New York legislature never gets anything done being good for a laugh from a Manhattan crowd.

I've read that John Adam's character was actually massaged a little bit to incorporate some aspects of Cousin Sam, so the answer to the question "Where's Sam Adams?" may be "-absorbed by his cousin John!"

I supposed they could have expanded the cast (and the script) to bring characters like Sam Adams back into the story, but usually when a movie is based on something else, they simplify, not complicate.

Massachusetts' delegation was a lot larger than lonely old John Adams anyway. There were enough others there that a majority faction wanted to stand with the South on the slavery clause in the Declaration. So that line about the "other end of that filthy purse string" isn't just a throwaway line, it had teeth!