My headcanon is that the holodeck is basically like a big replicator that you can play around inside. It can effectively create anything from the molecules up. That's why you can drink alcohol in a simulated bar, for example. Most of the time the holodeck is just used for fun.
If you went into the replicator for a camping trip, you might want to boil some water over the holodeck "fire", but most of the time it would be a simulated fire that didn't get hot enough to hurt you because of the safety protocols. It could simulate the look of the boiling water over the fire, and let you pour that into a teapot. Then, it would simply replicate some tea, earl grey, hot, into the teapot (at a safe, drinkable temperature).
In that case there's really no need to disable the fire or boiling water safety protocols.
But, what if the ship was damaged while out in deep space and couldn't easily get back home to a repair dock. You'd want some way to repair it. As far as I can remember, they've never shown the ship to have a machine shop, so maybe that's how they use the holodeck. Since those situations are really rare the holodeck is mostly a place for people to play around, but in a disaster you see its primary purpose.
For certain things, it can just replicate them directly, like say some antimatter conduit, it's just a room-sized replicator that can create big items. They even show the holodeck having a huge doorway, instead of just a normal person-sized door. Since the holodeck can simulate big things, presumably you wouldn't need to say drive a dune buggy into the holodeck because it can just create one inside. So, maybe the big doors are for taking things out of the room.
Maybe you don't need to disable safety protocols for that. You just say "replicate an antimatter conduit". Then Barclay and Jordi can carry it out through those big doors and put it where it needs to go.
But, there seem to be some things that can't be created by a replicator. I assume latinum can't because otherwise why wouldn't the Ferengi just create as much of it as they wanted. Also, if you could just replicate dilithium, a lot of problems would be solved, so presumably you can't do that.
But, maybe you can build a dilithium repair machine, or something like that. Now, if the crew is training how they'd use that kind of a machine shop in a disaster, maybe the safety protocols would be on, and out of the simulated machine would pop a simultated dilithium crystal. But, if there were a real disaster, you'd need a real machine, with dangerous electricity, dangerous antimatter, who knows what else. So, in that case, the holodeck becomes a machine shop where you turn off the safety protocols and real physics happens and you can do whatever's necessary.