It's certainly not an easy business. Most writers I've talked to talk about rewrites, and some of them have even been written out of their own original scripts. Any time you feel like you've been given notes that don't make sense to you, you should at least pause. There are two reasons not to do notes that don't make sense to you. Either, you don't like them, and you shouldn't do what you don't like to do, but the more practical reason is that if you don't like the notes you're not going to execute them very well.
Writers have to find a level between their artistic integrity and their practical needs.
Then you do the best you can. That's what happens in the vast majority of times screenplays are rewritten by another writer. In the Hollywood system, nine times out of ten, until you're a big star writer, and even when you're a big star writer, you're going to be rewritten. It's very rare to be the only writer on a project, for a million reasons, including the reason that studios don't always know what they want and they just feel more comfortable if the last person on the script is a big A-list writer. It makes them feel much more comfortable than relying on a young kid who they've just paid five hundred thousand dollars to because of the spec sale.