Sorry for the late reply--I PM'd you this information but thought I'd place it here as well for those who may be interested.
Several of my articles mention the issue, and you can find a detailed account in Michael Broggie's book, Walt Disney's Railroad Story.
In a nutshell, through the 1960s, the sponsorship fees increased dramatically, going from $50,000 per year in 1955, to $100,000 for the final five-year contract which ended in October 1974.
Concurrently, passenger train travel had declined significantly, and in 1971, Amtrak took over virtually all of the nation's passenger traffic.
Santa Fe was left wondering why a modern freight-only railroad should be sponsoring antiquated steam locomotives that pulled only passengers.
On another front, when Walt was alive, he had friendly relationships with several Santa Fe top-level executives. After he died and these executives retired, there was no more personal connection between the Disney Company and the Santa Fe.
All these issues conspired to end the sponsorship. The Santa Fe wanted Disneyland to have a diesel engine, which Disney executives (pedominately Marty Sklar) declined to even consider for obvious reasons. Disney told the Santa Fe that they would work up some new ideas, but only after the Santa Fe ponied up $112,500 for a two-year contract extension.
The Santa Fe was infuriated, and on October 11, 1974, the Santa Fe terminated the nearly 20-year agreement. Word went out to Santa Fe executives not to provide complimentary train passes to customers. Disneyland, on the other hand, sent the Santa Fe an estimate for removing all references to the Santa Fe from Disneyland's trains, tickets, station signage, audio spiels, etc. Santa Fe told Disney in no uncertain terms that it was under no obligation to pay for such removal. Basically, it was game-over at that point.
That is why the Santa Fe does not sponsor the trains any more, but at least four of the engines still bear their original names, all Santa Fe executives.
To answer your other question, Santa Fe sponsored the Monorails and the Viewliner as well. Retlaw operated the trains from sometime in the late 50s or early 60s until the early 1980s, when the trains were sold back to the Park.