Think of kunyomi vs onyomi like Latin/Greek/French vs germanic/anglo-saxon words in English.
“car”: germanic word
“automobile”: latin compound word
if english used kanji, the kanji would be 車, the kunyomi would be “car”, and the onyomi might be “auto” or “mobile”.
you know from english that there’s a whole ton of latin/greek roots, prefixes, and suffixes that don’t get used in words on their own, but get combined with other roots to create compounds, whether it be “automobile” or “optometry” or “astronaut”. Like for example, you’d never say “opt”, you’d say “eye”. But you don’t say “eyeometry”, you say “optometry”.
japanese works almost exactly the same as english does here; there’s one language whose roots are used for compound words (Chinese) and another for non-compounds (Japanese). so you can basically apply the same kind of rules as a starting point. the only big difference is that kanji exist, so you have a single symbol that gets used for both the compound word (i.e. Chinese or Latin word) and also the non-compound word (i.e. Japanese or Germanic word). this analogy holds surprisingly well IMO – for example, kanji compounds tend to be seen as more formal or fancy, like (again) “automobile” vs “car” in english.
of course, there are exceptions to all of this! but english has those too. and wanikani will teach you those as you go along, too.