Someone with this much responsibility in the private sector (essentially the CEO of a company with $2.55 billion annual budget and 2,700+ employees) would almost certainly make much more than that. For that reason, I tend to have a hard time getting outraged about paying very high level government employees with lots of responsibility a reasonable salary for that level of position (and still way below what someone similar in the private sector would get).

If you want a decent candidate with enough relevant experience to actually take these sort of jobs, you have to pay well. There aren't that many people out there who have experience leading a large transit organization.