as long as the increasingly expensive jet fuel currently in use remains, this won't happen
Plus there's the sonic boom problem, serious enough that major research is being conducted on it despite nobody actually planning on building supersonic transports (and few planning on building supersonic anything for the civilian market). Powering the transports with hydrogen or something else harmless wouldn't mean a breakthrough yet, not even if the technology proved to be dirt cheap to manufacture and use.
I doubt analogous problems would plague high-warp shipping, as space is big enough to swallow all pollution and congestion ever created by all the Trek sapient cultures combined. (The "warp eats holes into subspace" thing wouldn't be a concern yet, and probably will be ignored for millennia to come anyway, since it only applies to extremely congested spacelanes.)
It makes sense that unimportant freight would travel at lower speeds.
The funny thing is, all the civilian transports we have seen in the Federation era have been tiny things, supposedly hauling high-value, compact goods and items, and often quoted with high speeds (much higher than those of Kivas Fajo's pleasure cruiser, say). But bulk transport at glacial speeds might still survive - after all, there are references to galactic food shortage and to agricultural worlds, the combination (and its proposed solution through Genesis creating more of the latter) requiring extensive shipping of food.
Timo Saloniemi