Yeah cost is only one consideration, for me there are a lot of reasons that I generally choose not to take PT. It works ok for certain scenarios, but is usually the worse option by a significant margin. Even being free isn't enough to tip the scales the vast majority of the time, particularly when non-cost considerations are included.
My motorcycle gets me to work in less than half the time, leaves on my schedule, I know I'll get a seat, I can use the one vehicle for the whole trip, it's far more reliable, I get sick less often (thanks, people who take PT when they are clearly unwell), not to mention that I enjoy riding anyway which is in itself a decent incentive. Taking the car still ticks these boxes - it takes longer than the bike but is still far quicker than PT, plus I can take bulky/heavy things that simply aren't feasible to take on PT, and it's a negligible additional cost to take others with me. That said I'm lucky to have parking at work, if that wasn't the case it would be far less feasible.
And that's for the city-and-back trips that I assume PT has been optimised for. For any other trips, PT rarely makes sense, though PT being free does address the issue of paying separately for each passenger (eg 4 people going to the city and back costs ~$45 on PT, ~$10 in the car).
If I'm to actively choose PT over bike/car it needs to be the better choice. And it needs to do that by improving, not by simply adding barriers to alternatives.

A few things come to mind, with the caveat of course this is all from a layman's perspective and may be misinformed, dumb, or otherwise not feasible.
Basic stuff:
More ambitious:
There are no doubt tons of others but that's a start.