Part of the problem is that we've got a hodgepodge of roads, built at different times, to different standards. Rail crossings are also complicated, because the train companies own the rails and the land under them, so cities are largely unable to force them to make changes to their property.

In this particular instance, the tracks would need to be redone for a few miles on either side of the bridge to raise it, and the North Carolina Train Company just isn't willing to front the cost and eat the downtime. There's only so far you can dig down before you hit groundwater problems, so the city can't do much to lower the road under the bridge.