The museum land was purchased by the founding members pooling some of their own money, they were looking for a site to store the two cars they were fortunate to be preserving. The TSR right of way land was available for back taxes, which was pretty much all they could afford at the time. It wasn't like they had the money to buy land in Toronto somewhere but chose a remote rural location over that. As far as I've heard, there were no TSR buildings on the site and the former right of way had to be cleared of growth that had started filling it in since the line closed.
The attendance at the museum on the last Saturday of October during the day was almost 1,200, which was by far the highest attendance day of the whole year and likely in many years, so they aren't having difficulty in getting people out. Definitely a transit-friendly location would be better, but the best one can do is take the GO bus to Rockwood and an Uber/taxi to the museum. If the museum were in an "economically challenged" area (particularly in Quebec), federal government support might be available, but the GTA is far from economically challenged so there's no funding coming anytime soon.
The Ford Nation types wouldn't support funding at all. Denzil Minnan-Wong famously said "not one dollar" would be made available for a Toronto transit museum.