Yes, $50 is a bit steep for leaving a window open, you're right.
Now you give us your own suggestion for ending the dozens of occassions when so-called professional students don't comply with the check list and leave the window open, then a summer thunderstorm rolls through and soaks the inside of the aircraft - next person can't fly it till it dries out (and it stinks!!).
Drop a pen? That's not the *really* the deal now, is it!! I can't count how many times I've encountered aircraft littered with empty, but dirty, coffee cups, dripping cocoa-cola cans, discarded weather print outs and flight logs.
What do you suggest?
The school sends out a cleaner, at no cost to you, to tidy up after you and make it all pretty for the next guy? Quick valet service? Clean the windshield for you?
If you want to be treated like a professional then act like one. It's not a big job to take your rubbish out with you - nor is closing a window.
Of course the charges are Draconian - that's their whole point. Comply with the rental requests of the school and you won't have a charge, will you.