Let's call a spade a spade. It doesn't matter the situation of the agencies for which he works. Scanlon's compensation is out of line for his position.
Based on what?
He could probably make more in the private sector. Most of Caltrain's problems are out of his hands. I love the comments from people that say, "Pay me 100k and I could have Caltrain in the black in no time!" Good luck navigating the political realities of transportation funding. Their only options will be to cut trains, raise fares or some combination of the two.
In fact, Caltrain could be doing poorly in spite of Scanlon's best efforts. "It's the economy, stupid."