Several people seem to be under the impression that the actually information in books isn't worth very much, and unfortunately, I think we have publishers to blame for that. Books, as they are priced on Amazon for example, are not priced to make the author any profit. They are priced to benefit the publisher. The vast, vast majority of that low price goes towards the publishers ethereal and rarely specified "costs" (plus, they absorb about 80-90% of the profits typically). They can price things at such a low price because they make up for it in volume. Their costs actually go way down as volume goes up. Printing is much cheaper, especially if they're sending a steady stream of work to a particular printer. Editing costs don't scale linearly in most agencies. Support costs definitely don't scale linearly. So they can spread their costs around to several different projects and still make a boatload of money.
Independent authors, who are trying to actually make somewhat of a living off of their works, do not have such luxuries. They are the editing department. They are the typesetting department. They are their support department. They're doing all these things with no benefits of economies of scale whatsoever. So it costs more. This is also why academic presses tend to cost more, too, because they're operating on a much smaller scale.
I can appreciate the desire for a physical book. I, too, prefer dead trees. Some of my own readers prefer it too (and for some reason think for $12 [or less], they'll get it), but in reality you have to realize that in paying $39 or $69 for that PDF, you're paying for a lot more hours of work from one person, costs that aren't spread across an entire business like a publisher, and that money is going directly to the author who is providing the product, which means it's probably (not always) going to be of a higher quality and a better purchasing experience (i.e., you could likely e-mail Nathan with a question and get a reasonable response).
Also, the scale of marketing for an independent author is much smaller. It's simply impossible to negotiate with the bigger players for shelf space, and it's not profitable to invest in tons of streams of marketing typically. So, you're left to target the niches you're writing for the best you can and hope it works out in your favor. I've had fabulous successes ($50k+++) and horrible flops (< $1,000 for a lot of work). A lot of that is because it's difficult to saturate the general market and get them interested in your work. Very rarely will someone come over your book and say "Oh hey I've heard about Rails [or whatever]. I'll buy that." because most people aren't browsing the Internet using Google's "I'm Feeling Lucky." So for most indie authors who aren't selling like Nathan, the higher price is needed to justify the investment of effort into the book.
So, that wall of text is to say: please think about the person behind the book and the effort they're putting into it when you look at the price tag. Obviously, they want to make money. They're not pricing it to give it away. But likewise, they're also [probably] trying to feed a family and keep writing more books.