The cost of waypoints varies according to the distance from your current point to the selected waypoint.
I'm finding them more expensive each time. Now traveling to a near waypoint (near as in next to it) costs 85 copper. I'm not sure of how much did they cost when I started playing, but I find them increasing in price.
Is it just me? can anyone confirm this? Maybe the cost increases each level, or depending on the area, I'm not sure, but there's something else than distance to calculate the cost.