Activity Monitor, my system always runs in the red for CPU load - how to fix?
Your confusion is the result of a bad UX design decision on behalf of Apple. 

Basically, the red colour in the CPU Load graph within Activity Monitor signifies the level of CPU usage by the System. The blue colour signifies the level of usage by User processes.

In other words, red isn’t being used to signify danger, or to try to alert users to a problem, it’s simply the colour chosen to signify system usage. So, if the system is using 1% or 99% of the CPU, it will always be displayed in red.