One of my hobby horses is telling young bands not to do these deals but, to be honest, even old hands accept them and if a young band wants to play live they often don't have a choice.
That said, because I have done a lot of work on audience development for my main artist we have done door charge splits where we've given the venue more than £100. You could argue that "door less £100" would be better in those circumstances but in my experience guaranteeing a minimum income to the venue leaves them with no reason to promote. I'd rather give them a bigger piece of the pie in return for more work and comittment.
As you say, it's up to the two parties to reach a deal that they both feel happy with.