I've heard some rumblings to that effect too, so I called YARTS. They won't be posting their schedule for the summer of 2016 until the beginning of May, and there is no current plan to eliminate the hikers shuttle from what they tell me.
http://yarts.com/about/ 877-989-2787
So as you know, the hikers shuttle is basically Yosemite Valley-Tuolumne Meadows, then back. If it's safe to drop you at a trailhead, ie: they have the room to pull out with a big bus (think Greyhound sized), you can let the driver know and they'll accommodate you if they can. Scheduled stops are; Curry Village, Yosemite Village, Yosemite Lodge (or whatever ridiculous names they're going to call them now), then Crane Flat gas station, White Wolf, May Lake Junction, Olmstead Point, Tenaya Lake, and the Tuolumne Visitors Center. Anything else in between, ask...their drivers are masters at squeezing those buses into places you might not want to even drive your car into.
The schedule I have in front of me from last year is as follows- Several stops in Yosemite Valley beginning at Curry Village. They pick you up right in front of the lodge, and run 7 days a week. Leaving from there, the first bus is at 7:45 am, another at 8:45 am, then the last at 1:30 pm. They used to have a later bus at 3:30 pm, but they cancelled it. The hikers shuttle is free, and the last stop is the Tuolumne Visitors Center. There is also another bus that goes from the Valley Visitors Center leaving at 5 pm to Lee Vining. It costs a few bucks per person, but you still can't beat it with a stick.
In reverse from the Tuolumne visitors Center to the Valley; the first bus is at 10:15 am, the second at 1:15 pm, and the last bus is at 7:00 pm.
As I said, this was last year's schedule, so make sure to check back on their website or by phone when they post the new one in May. I make no guarantees on what they'll offer. You can also pick up a full printed stop-by-stop schedule at the major stops in both the Valley and Tuolumne.
And last but not least, there's the Valley shuttle, and then the Tuolumne shuttle that runs from the Tuolumne Lodge up to Olmstead Point in both directions every half hour or so I think it is.