The Strand in NYC, Powell's in Portland, and a number of more local ones at a smaller scale. New/used bookstores definitely aren't dead, they just survive in areas with more bookish populations (the entire city of Portland would riot for days if Powell's ever threatened to close).

I like the "treat it as a cultural institution and charge admission" solution, if that's what it takes to avoid closing. A few dollars would totally be worth it for an hour-long leisurely browse.