State-run trails, yes, in general, although there are exceptions. The locally-managed trails, no.
For instance, the Glacial-Drumlin is a state trail that runs from Waukesha to Madison. For most of its distance it is a fee trail, except inside of the city of Waukesha where it is free.
We just buy an annual trail pass at the beginning of the year, carry it with us, and don't worry about it.
Wisconsin is getting closer to its trans-state trail system. Right now you can almost get from the Illinois state border north of Chicago thru Milwaukee and to Madison via off-road.
But, as a road cyclist, the best riding in Wisconsin is on the roads west of Madison. Beautiful and challenging.