Tokyo manages a very tight schedule and they're enormous, so it can't only be scale that matters. And how do you fund effective transit in a smaller city with less of a tax base?

I haven't visited Tokyo, but I definitely plan to.

Regarding your question, if the city is made up mostly of apartment buildings & parks, with limited parking space available, almost everyone uses public transport.

There is obviously a trade-off between how pedestrian-friendly or car-friendly a city can be, thus if a city goes hard in the pedestrian-friendly (removing parking spaces, narrowing streets in the center etc.) direction, public transport becomes very attractive & convenient. Having a car becomes a burden.

Rail plus property model like in Hong Kong could be one (‘tax free’ zone…)