Jean habite la ville de Paris
In this sentence, why isn't there a preposition before la ville, like in the sentence: "Jean habite à Paris"?

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"Jean habite la ville de..." est tout-à-fait correct. Le verbe "habiter" est transitif. On peut donc dire "il habite une très grande maison, un peu à l'écart du centre". "Habiter" peut aussi s'utiliser avec "à" ou "en" : "il habite en Espagne".

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If you don't precise 'le ville de ' then you can use the prepositions à . Jean habite à Paris. In this case you precise that Paris is a city so then the sentence is completely different. In English It would be like Jean lives in the city of Paris versus Jean lives in Paris.

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To complete Michel, you may also hear sometimes "J'habite sur Paris" ou "Jean habite sur Paris". It's incorrect, don't use it, but lots of french speaking people make the mistake.

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It's not natural to say "J'habite à la ville de Paris". It's more natural for French people to say "J'habite Paris" or "J'habite à Paris" (both are correct).