But gratitude doesn't pay the rent. In all of the above situations, what the writer is being offered is a business deal. The person making the offer isn't doing it out of the goodness of their hearts but because they think they're going to make money from you. Perhaps we might start being a little less grateful...
Take literary festivals. The organisers are paid. The brochure printer and website designer gets paid. The venues get paid. But there's often no mention of payment for the author, or it's a nominal amount. And you'd have to sell 1000s of books to get back in royalties the cost of a lost day's work.
The agent and publisher - yes, they're taking a gamble, but they're doing it for business reasons. Lovely that they think you've got potential to make money for them, but unthinking gratitude? Why shouldn't you question the terms and conditions?
I was talking to a friend about garages and cars (I've had car problems recently). He said he wasn't interested in either, he just wanted his car to go. At his last visit the garage asked him to rate the service he'd been given. As he didn't tick "exceptional" he was phoned up to ask why. He said they had done the job they'd been asked to. That wasn't exceptional, that should be normal.
It's a bit the same for writers. You've done a good job and you're getting the appropriate response for it. You shouldn't feel grateful, but normal.