Just like windows has the differentiation between normal operations and 'safe mode', unix-y operating systems have a concept of 'run level' ... and you need to specify which run level should start the process.

The Unix System Administration Handbook is a good introductory tome, and the third edition includes linux.

Update: It seems there's now a Linux System Administrator's Handbook, which is cheaper, and more recently published, so I assume more up-to-date. (I haven't read it, but it's by the same authors (mostly))