^I'm surprised that you're unfamiliar with the doujin market. It's such a huge part of the manga culture.
What you need to know is that,
1-it's basically fanwork (...that existed before the internet), so there is an understanding that it is not made with the intent of copyright infringement and decreasing the original's sales. In fact, many authors view it as the opposite - a lot of doujins being sold are a sign that the work is popular.
2-they make money of it, yes (that is where it'd enter our concept of copyright offense) but most amateur authors barely make enough to cover the cost of the materials and booking a selling spot, and maybe a little for themselves for their hard work. You can actually make money if you're a very successful artist but even then you probably only sell copies in the thousands (there's no re-print and such; if you missed a doujin when it's out you lose), which is peanuts compared to the number of copies of the big magazines. In other words, you aren't viewed as a threat as a competitor.
Maybe you can try reading
"Doujin Work"...I also has an interesting
forum thread on this same topic.
