Yes, that part of the film was altered. It used to be a Pepsi sign you flew by, until about a year and a half ago (by my calculations). I noticed it first at the USH ride (thinking "Hey, thats different from back home!") and then a few months later at USF.
Pepsi was one of the big product placement sponsors for the BTTF movies, but Universal dropped them over Coca-Cola as the official park soda. Then a few years back, Toyota became a big time sponsor of the Universal parks (ever see those Toyota cars at the parking garage juncture, or parked on the New York street sets) and specifically, a presenting sponsor of the BTTF Ride (remember the Celica Time Machine) and the Spider-Man ride (the SCOOPS have Toyota stickers on them, and note the Toyota Spyder, with a web paint job, parked in Marvel Island).
The BTTF ride film plays so constantly, new prints of the film have to be created frequently. I guess Universal took the opportunity during the creation of a new print to digitally add the Toyota sign over the Pepsi one (also, from a source, they took the opportunity to remaster the film too). A couple of years before that change, Universal covered the Pepsi sign with a Coca-Cola sign for the Japanese version of the ride (Coke being a big sponsor for that park).
You can tell the Toyota sign is a digital addition, and not something created during the original production, because it has a "neon light" strobe effect. With the stop motion and scale model techniques used to create the original film, there was no way to animate a sign like that.
Though, for continuity sake, I should note that Toyota was also a main product placement sponsor of the original BTTF movie. They paid a lot of money to have the truck that Marty pines for at the beginning of the movie (and that he miraculously owns at the end of the movie) be Toyota brand.
Now you know that Texaco sign that we crash through right before of after the Toyota sign? Well, Texaco was also a product placement sponsor of the BTTF movies, but Universal also dropped then as a park sponsor a number of years back, in favor of Hess (the current Hess gas station on Sand Lake Rd used to be Texaco; the boat gas station in the lagoon used to be Texaco, and is now Hess; and I think the Hess gas pump that explodes during the Twister attraction used to say Texaco). So why don't they also alter the Texaco sign in the BTTF ride, to make it say Hess, like they did with Pepsi/Toyota? Because that Texaco sign crash is actually a transitional effect in the ride film. The whole film, as we see it, is one long take, but the filmmakers had to break it up into sections to film, with invincible cuts in the film. Other such cuts occur when we crash into the Clock Tower, when we fly down into the volcano and all that fire shoots up, and when the dinosaur swallows us for a second. So for Universal to digitally change a crucial transitional effect of the ride would be too much hassle (and Hess is probably not a big enough sponsor to bother doing that for).
I know, this is more then you asked for, but that what happens when you ask a BTTF question within earshot of me.
-Kevin