Toronto began offering higher order transit service since 1954, with the opening of the Yonge Subway Line which runs from Eglinton to Union Station in the south of the City. Vancouver has had a higher level of transit service since 1986, with the use of the ICTS technology which also operates on the Scarborough Rapid Transit Line. Toronto has a higher percentage of its workforce working in a single area, the downtown core between Yonge and University, on which the transit system is focused.
Vancouver has a higher number of people who live close to work, and a poly-centric layout. The transit system reflects this: It doesn't all converge on one point; it connects all the dots in an almost-loop, with a few tentacles.
According to the NHS Metrics as follows:
In Toronto Proper: 52.9% commute in vehicles, 36.5% by transit, and 9.4% by active transport. Average commute is 30 minutes.
In Greater Toronto: 69.9% commute in vehicles, 23.3% by transit, and 5.7% by active transport. Average commute is 30 minutes.
In Vancouver Proper: 51.6% commute in vehicles, 30.0% by transit, and 16.9% by active transport. Average commute is 21 minutes.
In Metro Vancouver: 70.8% commute in vehicles, 19.7% by transit, and 8.1% by active transport. Average commute is 26 minutes.
Vancouver appears to have less transit users because it has more workers who walk or bike to work, but the differences between the two cities in terms of vehicular commuters is almost negligible, and when the Evergreen line opens in 2015 (one year before the next NHS), we will likely see Metro Vancouver's numbers drop even more.