The main Thruway ticket system has approximately that rate (for NY E-ZPass), but the MassPike is actually closer to 7 cents per mile for an out of state E-ZPass.
I regularly drive between Albany and Rochester to visit family. The tolls are $9.50 (approximately) each way. The trip (round trip) uses about a tank of gas, which I can usually fill up for about $25, so the tolls add quite a bit. I can't say I've ever factored in per-mile maintenance into the cost of a roadtrip, but I do know that tolls are the biggest in-your-face expense I have (since gas stations don't tell you how much the tax is, and my car only holds 12 gallons anyways, so the price of gas would have to swing by a LOT for me to notice).
In any case, it's still odd that I have to pay more to go to New Jersey, Boston, or Syracuse, while Binghamton and Montréal are "free".