FWIW despite not having been in school for nearly 2 decades, I take a few short notes on all books I read in a personal wiki.
I don't do this as I read, but after reading the book. Or sometimes a couple times while reading the book if it's particularly interesting. If you do it as you read, you may fall into the trap of taking too many notes. And the forced recall after a few days improves retention, rather than a recall after 5 minutes.
Crucially, I connect the ideas to other books and Internet articles I've read. It's surprisingly easy IME to let keep a book in a knowledge silo; only by connecting the information will you actually learn something.
For example, I read both Nate Silver's Signal and the Noise, and Taleb's Black Swan / Antifragile, etc. Both of the books are roughly on drawing conclusions from data with statistics (or really the limitations of statistics in the latter case).
But if you don't actually compare the two books then it's pretty easy to read but not understand. I don't claim that I understood everything, but certainly taking a paragraph of notes is better than nothing.
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Paul Graham has a nice essay about whether you actually remember what you read!
http://www.paulgraham.com/know.html
I also recall reading a NYTimes piece about this. It's good to wonder about your retention, like the author of this blog post is. Although like others, I don't agree with the title. I think it's entirely possible that many people are not good readers. That is a skill that has to be taught -- there's a reason that every child in the states is MANDATED TO DO for ~12 years. And it can be done poorly, or it can be done well.
I think if you don't actually check if you know something, then you don't know it. So I think I agree that many people could improve their retention of books with a few small adjustments to their process.
People are reading and writing more than ever with the Internet, and I generally view that as a good thing. But I suppose it wouldn't be surprising if the retention of long form books suffered due to that development over the last couple decades. People learn to read earlier and "informally" rather than in a more deliberate fashion.