In terms of things that a transit agency or transit planners can actually change, the biggest reasons are:
1. The extent of Toronto's 10-minute-or-better frequent bus and streetcar network, and the fact that all but one surface transit route connects to the subway. This has been discussed to death on this forum;
2. The design of almost all subway stations as intermodal transit terminals with bus transfers within the fare-paid zone, rather than getting people to exit the station and board the bus on the sidewalk;
3. In the 1950s and 1960s the TTC mostly built subways underneath existing commercial streets while the CTA built el lines in the medians of freeways that ripped through communities. Toronto built one extension in the median of a highway and, relatively speaking, it's kind of an underperformer;
4. The headway of the subway itself, which is <5 minutes even during evenings and weekends;
- A relatively minor contributor, but one that actually puts Toronto's situation in a bit of a negative light:
5. Most of Toronto's bus routes terminate at a subway station, even when the road continues past the subway, so people are forced to transfer at the subway station to another bus to continue their trip on the same road.
Here's an example. If the bus ran past Yonge, you would only have to make 1 transfer rather than 2.
This increases subway ridership, even if the user is no better off.