Rooting is no different than having admin access on a PC. Just like a PC, you can mess things up.
Rooting isn't to install "back door" programs, it's so that you can have FULL control of your phone. Like a PC, if there is a program you don't like, you can delete it.
Like a PC, you have to be careful what you do. You can easily delete the system files that make everything work.
It's up to the user to be aware of the risk involved. For example, it voids your warranty. Like anyone else in every other aspect of life, users are responsible for their own actions. We as a community try our best to help users out. Just like a PC, you need to be aware of what you are doing and the risks involved.
Rooting CAN prevent OTA updates. That doesn't mean you can't ever update the phone though!
You'll be hard-pressed to find any one say "Root it without doing research. Jump right in without knowing the risks involved!"

We're all here to help and answer questions but the questions need asked.