Maybe the two words 'have the same root, but it is still just coincidence for them to end up so similar, and hence confusing to to people.

The word capital obviously stems from the Latin word for head (or chief), which makes perfect sense. The Capitoline Hill in Rome was however named long before the site had anything to do with being a capital. One myth says that it got its name from a human skull found in the ground when building a temple. But in the end the hill could have been named after a finger or a leg or whatever, which would have been so much easier for Americans.