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The taxing was done on a state by state basis. Some states, for example, have passed a law allowing them to tax any Amazon purchase (many states are trying to add this.) They used any Amazon associate as a "presence" in the state--to say, "You have someone doing business in the state so we can charge taxes on all business." Amz responded by canceling amazon associate businesses (putting some people out of business as it was their income).
That particular rule is being argued in most of the states now as every state is going after some "past" revenue and future.
So the answer to your question is complicated, but it basically had NOTHING to do with the publishers--because Amazon was considered the retailer so the only thing the states looked at was whether Amz had a "presence" in the state. The agency model, however, changed Amz status--they were no longer the seller so it only mattered if the publisher had a presence.
I didn't have to pay taxes on ANY book from Amz before the agency model. Now I get hit with 8.25 percent on some books. This really annoys me when I'm considering buying a "full priced" book - which for me is in the 8 dollar range. I can buy from Amz in mass market at 4 for 3 books and free shipping and get a better deal if I'm looking at new books. So if I know about the tax, I stick that particular book into the "maybe" pile for buying as a print version with the 4 for 3 -- or I look for it used. For an 8 dollar book, I can usually find it used for 4 dollars. I just have to give up the instant gratification of downloading it to Kindle and reading right away.
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