What made the Romans choose to destroy such cities as Carthage and Jerusalem rather than simply colonise them?

I don't fully understand what you mean, and I suspect it's because you're using the word "colonize" in a modern sense. To a Classicist, and in a Roman legal context, colonization is a very different thing than occupying conquered foreign territory. A Roman colony was an all-new foundation (or occasionally a refoundation, usually over a destroyed site) established in an area and inhabited at first by Roman citizens transplanted to the new city, then later by Latins without full citizenship rights (although citizens' colonies continued into the Principate). Originally most colonies were Italian, primarily in Latium, although by the late Republic and the Principate we see the rise of veteran colonies. But these aren't colonies the way, say, India was colonized by the British. It's a very specific type of urban foundation--not all provincial cities were colonies (and few, in fact, were) and most colonies were in Italy, not the provinces (although by the Principate their status as colonies had long since passed). Sometimes existing cities might be refounded as coloniae, which gave them special rights equivalent to their citizen or Latin status. If we still mean coloniae then Carthage was in fact colonized only a couple decades after its destruction, when a colonia was established there under Gaius Gracchus. This attempt proved abortive, for political reasons, but Carthage was refounded as a veteran colony by Caesar and the project was completed under Augustus. Jerusalem likewise was refounded as a colonia in 135--part of the cause of the Jewish Revolt of the 2nd Century was that Hadrian had established plans to refound the city as Colonia Aelia Capitolina, with the dedication of a temple to Capitoline Jupiter on the spot where the Temple already stood. Following this revolt the plan was carried out in modified form, and the city was refounded as a colonia--but it had existed for nearly two centuries as a client-city and then later as a regular provincial city.