depends on the pizza/toppings, and even then i have some variance
I would concur. If I'm making a Chicago deep dish, the toppings go under the cheese, but I don't make them that often.
Most of the pizzas I make are what might be called a NY/American style hybrid, with a relatively thin crust, so light to moderate cheese, with toppings on top. I also like how meat like pepperoni and sausage crisp up when they are on top.
There is a great family run pizza place near where we used to live in LA. They were one of the few pizza places I've eaten at that put the cheese over the toppings, which made it quite a soggy affair, even right out of the oven. So, I started ordering the pizza with the toppings on top, and the difference was night and day.
Here's two pictures of 2 pepperoni and meatball pizzas, from the above establishment showing one with the cheese on top, vs another with cheese on bottom:
I understand some folks like it differently than I do, perhaps the melding of cheese and toppings makes it more casserole-like. I prefer the separation of toppings from cheese, which makes them stand out more individually, if that makes sense.