I think there's 2 reasons...
1) Roeder stated that he wants to retain control of his books, something an author gives up when publishing with a company.

2) Roeder's work is a bit too taboo for most publishers in the young adult market. His earlier works are a bit repetitive (how many times did he say that Brandon loved Casper's 'inner' beauty? it has the making of a drinking game) AND his characters are a) more sexually active than you find in other YA novels b) lived rather gritty lives -- suicide, incest, physical abuse, disownment, rapes, prostitution... real things but as a reader of LGBT YA novels, I don't know of any book that compares.

BUT, these topics are important. So many gay teens go through just these issues and don't those teens deserve to see themselves sensitively portrayed in print as much as teens with "perfect" lives. So it's wonderful that Roeder is writing them and putting them on the internet for free so closeted teens have access without the evidence!