You compare an idle doodle to a full production. This is not an accurate comparison. A more apt comparison would be to compare an idle doodle with a rough draft of a script that never makes it to production.
Doctor Horrible's Sing-Along Blog has been well received and in my humble opinion I see nothing wrong with them cashing in on it a bit.
If an artist makes something and no one enjoys it, they get no pay. But when they make something that people enjoy then they do typically receive monetary compensation for said item. The same is true of this production. People do enjoy it, so they do deserve to make some money on it.