The problem is that vehicles in general cause negative externalities that the people driving them don't pay for, namely: Traffic congestion, localized pollution, and global pollution (CO2). FHVs are definitely susceptible to this phenomenon. Here in NYC we're having to implement a congestion tax in Manhattan to reduce the number of vehicles on the roads.

Admittedly, it is probably better to charge all vehicles for entering the most congested areas by their size (i.e. trucks pay more) than it is to pick and choose by artificially limiting just some types of vehicles while allowing unlimited numbers of others.