I think it's a tradeoff between giving the program functionality and avoiding making people nervous. For example, HotkeyNet has the following features:

1. People can trigger hotkeys with any combination of keys such as A B C.

2. People can trigger hotkeys on a key release, not just a key press.

3. Hotkeys can swallow the trigger key press so it's not seen by the foreground thread.

In order to put those features into HotkeyNet, I had to use either a hook or a device driver. Perhaps this scared off some potential users. To avoid scaring them off, I could have decided not to use a hook. But then those features wouldn't have been in the program, which would have made it less appealing, which would also have lowered the number of users.

In weighing those two factors, I don't think the first one is significant. I think very few people worry about hooks or even know what they are.