The Twin Towers, when they were built, were the tallest and second tallest buildings in the world. The new World Trade Center, though taller than the Twin Towers, was not and has never been the tallest building in the world.
The World Trade Center's main claim to fame, however, is being the center for world trade. It is to world trade as the UN is to world politics. That is why it was the target of not just one but two major terrorist attacks, not to mention numerous other thwarted attacks. The World Trade Center, then and even still now, is a target for anyone who demonizes world trade and believes that the US's economic dominance in the world is the source of their woes. Those dangers and seeing them realized twice in 10 years are why there was serious consideration given to not even rebuilding it, to no longer having a centralized location for conducting world trade. Its great fame, or great infamy to attackers, as a centerpiece for world trade is why it has been a target, not because of any fame for being particularly beautiful or tall.