Not everyone wants to be told what to do, all of the time. Sometimes help messages can come across this way, as instruction rather than assistance.
Many parts of a website or software program often require some sort of notification or tooltip to instruct the user of how that particular function works. This is a fact and rightly so should there be a help message in these instances.
But when help messages become a feature in and of themselves, then the developer may have gone too far.
The best way to discern if you may be putting in too many help-messages, and potentially annoying the end user is through testing. Other human testers will be able to let you know if they feel they are being ‘hand-held’ through the software, and patronised in the process.
After all, the software or website is going to be used by a human. It makes sense not to annoy him or her unnecessarily.