At one time, Burger King ran an ad that there were a thousand ways to have your Whopper. (ten condiments that you could have or leave off, I think.) If you're not going to back that up by actually doing it instead of just making assembly line burgers, don't advertise that.
And McD's, which is what Sparky McNosalt up there was talking about, has never advertised that. BK's pretty much always stressed the "have it your way" thing, because when they and The Clown were the only games in town, that's what set them apart.
So, yeah, if I go to BK and I want no onions, I order it without onions. If I go to McD's and I want no onions, I suck it up and scrape them off.
Every Friday I hit up my nearby Wendy's to get a value menu bacon cheeseburger, ketchup only. I've never gotten any guff or any extra-curricular stuff in my sammich, possibly because they know they're getting my money each week, and maybe because that's a really disgusting thing to do.
Wendy's has also been all about the "we make it fresh and to order" thing, too. Really, most burger joints are anymore, aside from the aforementioned Place Where The Cool Hang Out, Swass Play, And Rich Flaunt Clout and McD's, which is why I mentioned the Quarter Pounder in the first place.