I am working through Genki 1 and noticed some of the vocabulary words like 勉強する and 結婚する have a base noun and する appended on the end to indicate doing the action. My question is, can I do the same for other nouns to indicate doing the action. For example, would 運動 する（うんどうする）mean “to do physical activity”, or is what I wrote just gibberish? If I can, then what rule should I follow for appending する to the end of nouns, and if not, why was it okay to do with the first two?
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Some verbs are する verbs. They are nouns if you get rid of する.
If you use a dictionary it says which verbs work this way.
In your example let’s look at the dictionary:
https://jisho.org/search/%E5%8B%89%E5%BC%B7%E3%81%99%E3%82%8B
See there how it says:
> Noun, Suru verb, Transitive verb
That’s all good information for you. It can be a noun, or a verb with suru, and when it is a verb it is transitive.
Transitive vs Intransitive is covered later in Genki so don’t worry about it yet.
Not all nouns can have する. If it just says “noun” in the dictionary entry and not “Noun, Suru verb” then it’s stuck as a noun only.