But random towns in the middle of nowhere are not connected by such highways.
Speaking as someone who ran over a deer a few months back on a smaller road that connects these community. All kinds of animals cross these roads regularly and usually without impediments, can't be said for an interstate.
You could just have dirt roads. The problem isn't the road per se it's the crazy fast cars on the road. If cars rode at 12mph like they do on dirt roads, at about the speed a deer can gallop, that's like 25x less kinetic energy and if you hit a deer it'll bump and keep going.
Highways and interstates are problematic, yes, but they often take away lands in suburban areas as opposed to the wilderness.