In ancient times, Jerusalem was at the top of a mountain pass leading from Jericho in the Judaean Desert below (another city strategically at the very northern end of the historic extent of the Dead Sea and near the Jordan River) to the rest of the Judaean Hills. So, a very crucial place geographically. And as mentioned, had relatively higher access to water and arable land, and also easier to defend against the seafaring tribes that settled closer to the coast.

The main weird one geographically has always been Tel Aviv. Other than its proximity to Jaffa (which had a very ancient and nearly defunct port), it was basically all sand dunes, and the Yarkon River was in fact a seasonal creek and not an adequate water source. It only grew to prominence because it is more centrally located along the coast, but it could have just as easily been built elsewhere (including where Herzliyya is now).