We must remember that the current Grand Canyon Railway was founded by avid rail fans who invested a lot of money and took on very considerable financial risks in building a business model that took many years to become profitable. At that time, it was definitely prudent to reach out to all possible avenues of revenue (especially rail-fanning Amtrak passengers) to be part of their business plan. It also was the goal of the GCR's founders to "restore" the Williams connection with the Chief as Santa Fe did when they built their replacement depot at WMJ depot when the mainline reroute was completed between Williams Junction and Seligman.
However, Xanterra (the primary concessionaire at Grand Canyon NP on the South Rim) purchased the GCR about 10 years ago to build up their NPS concession holdings nationally. Since Xanterra is profit-driven from traditional state and park service income sources (lodges, restaurants, campgrounds, sightseeing tours, etc.) and providing a public service to many non-concession users, such as Amtrak passengers seeking an alternative to FLG, dropping the Williams Junction Amtrak service doesn't surprise me all that much. In the early days that Xanterra owned GCR, many of the managers and employees were kept to run the business under their ownership. However, over the years, I assume that many of those people have retired or moved on and many non-railfan focused managers now are operating GCR these days. Although dropping the service will be disappointing to those who use it, I honestly don't believe dropping WMJ shuttle service will have any negative impact on GCR ridership. Amtrak passengers who want to ride the GCR can easily book one of the many scheduled Amtrak thruway trips between FLG and WMA. The biggest setback will those who wish to travel to FLG from points east wanting to stay at GCR hotel the same evening. I don't believe a shuttle is scheduled to depart for WMA after the arrival of the westbound Chief. Therefore, those passengers will have to overnight in FLG or hire a taxi to take them on to the GCR hotel in WMA. Fortunately, the eastbound Chief connects to all shuttles going to WMA and GRB, so same day connections remain possible, albeit you probably can't count of taking the GCR train the same morning up to Grand Canyon. Those who booked a same day connection to the GCR from the eastbound Chief were probably so far and few between anyway. Most people I believe would want at least one night at the GCR hotel in WMA prior to starting the long day taking the train up and back to Grand Canyon plus the touring at the park when you are there. A same day connecting Amtrak passenger isn't the customer Xanterra is marketing for anyway, plus it's not advisable anyway to try and schedule any same day connection between a long-distance Amtrak train and something like a cruise, flight, or travel package on the GCR. However, if Xanterra or Amtrak were to request a late night shuttle departure from FLG to just WMA versus all the way to Grand Canyon for westbound Chief passengers with AZ Shuttle, then the loss of the WMJ shuttle for Amtrak GCR connecting passenger would be mute.
In many cases, when a longtime Amtrak service ends, it has a long-term negative consequence on ridership and customer service marketing (the short-sighted idea that unstaffing Amtrak stations is good for business comes to mind right now). However, in this case, I believe the elimination of the WMJ shuttle will have little if any effect on GCR's ridership and Xanterra will continue to market its Grand Canyon products to Amtrak passengers using the full-service Flagstaff station as its connecting point. Simply put, FLG is a much better connection point to the Chief for GCR passengers in grand scheme of things. As a full service station, with ticketing and baggage, restrooms, plus a full-service regional visitor center on site. It is located downtown with multiple restaurants and shop all within short walking distance of the station. Unlike a lot of mid-sized cities, Flagstaff's downtown is very popular with locals and tourists alike. Plus, taxis and app-based rideshare services are available and many hotels in the area have guest shuttles that regularly travel to and from the station. Although the Hertz rental car desk is no longer there, renting a car in FLG remains relatively easy since most rental companies have offices in town not far from the station. By eliminating the GCR Amtrak by outsourcing to already established thruway services provided by from AZ Shuttle which will continue to stop and service the WMA bus stop, which is the same site of the GCR shuttle at the front of the GCR hotel, the GCR will remain directly accessible to Amtrak passengers using a 20 mile shuttle connection versus a 3 mile one. Although it is not the intention, by eliminating the GCR shuttle service from WMJ to FLG, Amtrak's schedule of connecting services with the Chief may better demonstrate the excellent connectivity to final destinations like the GCR, Grand Canyon NP, Sedona, Phoenix and PHX Airport traveling through FLG on-board Amtrak. In the end, Xanterra simply has removed the passenger service issues of late trains from their responsibility back onto Amtrak, where the FLG station agent can handle those issues more effectively, without eliminating their ability to market and sell packages providing a direct thruway shuttle connection from Amtrak to the Grand Canyon via the GCR.