Except that the vast majority of people have no control over when they have to be at work or when they can leave.
No, not directly. Although the employer is going to have to learn to be more flexible or move locations if they start losing employees because traveling to work becomes cost prohibitive.
It isn't as simple as just raising toll prices until people find a way to either drive less or companies relocate. It also isn't good for your tax base if you drive out companies.
However, the costs of maintaining roads has been going up, and the gas taxes have remained a constant number of cents per gallon rather than rising with inflation. Something does have to change.