That's a shame, but I wouldn't go nuts about it. The fees are quite cheap. And there's a bigger issue afoot here - some want the Thruway Authority to divest itself of the Canal System, citing the "fact" that the canals are only used by rich boaters and contribute little to the revenue/upkeep of the Thruways...
I wrote a letter to those Communists at AAA which (of course) they didn't print, in response to an article to that effect in their recent magazine. I reminded them that (1) MOST of the boaters that use the NYS Canals are blue collar people with relatively small boats and pontoons, and (2) people like me DRIVE ON THE THRUWAY with our trailerable boats, paying tolls along the way, in order to drop our boats in the canals and adjoining waterways, and (3) larger non-trailerable boats still patronize those towns along the Canal (which coincidentally are also along the Thruway) as they pass by, which could use all the income they can get these days. I reminded the AAA people that if NY doesn't want me to spend my recreational boating dollars here I'll be happy to trailer my Glastron to some other more boating-friendly state, pay its highway tolls and patronize its merchants instead...
So, perhaps paying the tolls on the Canal is worth it in the long run, if the bean counters in Albany will then leave things alone regarding stewardship of/funding for the Canal System...