Welcome to FT.
I am surprised you agreed that a $60 charge for thirty minutes of waiting time was fair, that seems very high to me (taxis in my town charge $24/hour, not $120). Perhaps it was more than thirty minutes. Either way, given the model of shared van services, it would have been fair if he had to leave, in accordance with company policy.
I am not sure what you meant by, 'he decided I now owed him $101'. Why did the amount go up? Was he raising the 'waiting fee' or was the $41 for the ride itself?
I would certainly send the company an email. Be honest and clear about what happened and what you were charged. If the driver was doing the right thing, the company will rightly support him. If not, the company should be grateful for the inside story on how their driver operates. I see no risk in sending the email.
Lastly, anybody who says to me 'and don't forget my tip' just ensured he won't be getting one.