Well one way to do it is to make these routes the remnants of an empire, like a lot of post-apocalyptic D&D settings. You have nice Roman-like roads with bridges. These could be patrolled by locals. This would allow for safe travel between close towns and, at least a faster route through the wilderness.
Then I started thinking about canals. Has a D&D setting ever used them? They would be perfect for a Western Marches style game. You discover an oddly straight waterway, even though over grown, banks crumbling, and you know it will lead to something interesting. Probably both ways.
|Canal going into a tunnel|
Canals and locks leading over a mountain seem a perfect way to get over a mountain with horses and gear in a much safer way. And a perfect reason to go into the mountain ruins: to try and get the locks and reservoirs working again.
|Towpath cut into stone|