I think it is important to note that the original poster has submitted proper requests to the manufacturer for prototypically correct items, and championed the cause for the Milwaukee Road S-2 Northern and a Timken 4 Aces locomotive. And as explained in forum posts past, he has researched those locomotives and gone as far as hand delivering that information to the manufacturers at York.
Now, as I've thought about this more, I think what bothers me isn't so much the branded trains - M&M's, Harley Davidson, Bart Simpson, Hogwarts, etc. That's advertising and it makes sense, and has a broader appeal, even to those outside the general train hobby. Lionel Lines doesn't bother me in the least either.
What bothers me is waiting for an item to be produced in a particular road name, and then when something is produced in that road name it comes with goofy graphics or is painted in a non-prototypical color. For instance, MTH made a Nickel Plate hopper in the same blue color as the Alco PA's a few years back. There isn't much NKP rolling stock out there, and when something did get produced it was produced in blue and not a traditional black paint. I'm not a rivet counter, I realize they are toys, it was just disappointing more than anything else because it wasn't what I hoped for.
For those that can and do paint their own cars it may scratch the itch for what they are looking for (at least that's true for me). And it's opened up a whole new avenue of the hobby and taught me how to do things I didn't think I could with painting and detailing. But that's not everyone either, there are many who just want to run it right out of the box.
This hobby is wide ranging and that's a good thing. I don't begrudge anyone for running what they like, but I do understand the disappointment, of seeing "fantasy" paint on items when your hoping for something a little closer to the real thing.