That's a loaded question. It entirely depends on who you ask as this topic is shrouded with conspiracy theories and differing opinions. If you want to go with what the American Government wants us to believe then this is why -
Osama bin Laden the leader of the Al- Qaeda terrorist faction from Afghanistan declared a holy war against the United States.
The attack on the towers was retribution for religious atrocities that America had perpetrated against Muslims/Islam throughout the world. Such acts include US support for Israel, the continued American presence in Saudi Arabia (home of Mecca) after the Gulf War and their involvement in sanctions in Iraq.