The problem of freeways (and other blockades) cutting off the movement of people (who are not in cars) and animals is not new. And there hasn't been a lot of attention given to solving the problem—just ask anyone who's ever stayed in a motel and tried to get to the restaurant across the road on foot.
Some cities have introduced overpasses and underpasses in pedestrian-thick areas, like universities. But only in money generating ones, which is why there often aren't even sidewalks in poorer neighborhoods. So non-human animals who need to cross the road? Well, tough luck.
Some activists, tired of seeing massive amounts of animals hit by cars even in so-called "preserves," are campaigning to build over and under passes for deer, alligators, panthers, and salamanders. I'd heard about land bridges over I-78 in the Watchung Reservation area of New Jersey, and heard that auto accidents on that stretch of road decreased dramatically, with no reported collisions with animals. Proposals for a similar project to allow coyote and opossum to safely cross the Sepulveda Pass in L.A. was met with scorn, even from environmentalists, who wondered how animals would find their way there. But apparently the oldest land bridges (and tunnels) built with wildlife in mind are in the Everglades, and both humans and animals seem to be appreciating them.
I don't know how the animals find the best hikes, the best bridges, the best bicycle paths, either, but I'm sure once they do, word gets around.