Outside of bridges and a few true toll roads, road tolls seem to seldom be about cost recovery. It's about, essentially, punishment: if you want a nice thing (ability to bypass the proles) you have to pay extra for it (beyond your normal tax load). EPA likes it because they think it discourages driving; one of their traditional transportation control measures has been tolling the approaches to central cities, in an effort to make it more expensive to drive than to take transit.

To the extent that tolls yield funds in excess of the cost of collection (which they usually do, especially when set at levels seen in Northern California, and applying to HOVs (2+) as well as single drivers), they might provide funding for other programs like bike lanes and transit improvements - transparent accounting and auditing seem to be lacking. So they might be treading a fuzzy line where they could be considered taxes - which has not yet been investigated but could be dangerous for the programs if not properly voter-approved. At least the high bridge tolls in the Bay Area, which are in fact intended to fund other things as well as paying off bridge bonds, were voted on. Not so much the "express lanes" tolls.