You can see "timid" in the middle of intimidate, and to be timid is to be frightened or to pull back from something. When you intimidate, you frighten or make someone afraid. A pet rat might intimidate your sister's friends, keeping them out of your fort.
"To frighten" or "make fearful" is at the root of the verb intimidate. An animal might intimidate a smaller animal by bearing its teeth, and a person can intimidate another by threatening to do something harmful. You can be intimidated with mental or emotional bullying, as well as with something physical: "they were all good spellers, but some of them knew how to intimidate the competition into thinking they didn't have a chance at winning the spelling bee."