do cycle facilities piggyback on roads for autos?
In Toronto the main types of bike route are:
Bike lanes and/or 'shareways' painted on a few of the second-largest roads: so that a few of the major roads have bike lanes
Recommended (mapped and sign posted) bike routes through minor, low-traffic, residential streets (which have lots of stop signs but little car traffic)
Apart from those there are mixed bike/pedestrian paths, paved but forbidden to motor vehicles - through parks, along rivers, and along the lake shore ... and, in one place, along a railway line.
non-car-related bicycle facilities
There's some cooperation with rail. There's a railway system that brings commuters from nearby towns and suburbs into the city. The most important, central station is in the downtown core. One of the more recent bits of bike infrastructure is a bike storage room in the central rail station, intended presumably to let commuters store their bikes there: to live outside the city, take the (crowded during rush-hour) train without their bikes, and to have their bikes when they arrive (to get from the station to wherever they work).
As for public transport within Toronto, you're not allowed to take a bike on the subway during rush-hour; but the buses (all the buses, I think) have convenient bike racks.
(See also bike paths, mentioned above).
how does it happen
Here's a link to Toronto's published bike plan: including the plan, the consultation proess, etc.
There are disputes in city council (published in the local papers) about whether to have a bike lane on one particular street in the downtown core: some people would prefer to reserve it for a higher flow of cars. It seems to me that there are enough bike routes everywhere except in the downtown core, where there are few or none (enough for me, though the majority of other people don't cycle, perhaps partly because they find it too scary).
FWIW there are occasionally similar disputes (which local residents and apparently especially local shop-keepers get involved with) on various other streets, about routing tram lines, and about whether to allow on-street parking.
The current mayor is said to be anti- or at least not pro-bike, but isn't going to remove the controversial bike lanes. There have been bikes in Toronto for much longer than there has been a bike plan (the plan is recent as far as I know: someone must have said, "we need a plan"). I think the current plan pre-dates the current mayor, but I'm not sure.