Vocaloid culture, Touhou, Cave Story.. immediately come to mind as doujin that became a hit in the world at large and aren't pornographic in nature. There are many that Western audiences never even know of.
Many visual novels too, though they may include sex, aren't really focused on porn, just like the many Hollywood movies that contain sex scenes are not "porn."
You forgot to mention it's mostly because doujin is pornographic in nature. That's why it's so big. Now if you were to classify pornography in a separate category, well the numbers would look much lower.