I recently finished the book "Looming Tower" which chronicled the developments before Al-Qaeda's attacks on the World Trade Center, the attack on the USS Cole, and also the attack on the US embassy in Kenya. One frequent narrative from several sources in Yemen is that the US should expect such attacks for "occupying" Muslim holy lands. Can anyone shed light on what this meant? Did it refer to US support for Israel? The US presence in Saudi Arabia during the First Gulf War? What?
The specific controversy that is being referred to was related to the significant presence of US troops in Saudi Arabia (which contains the two holiest cities of Islam, Mecca and Medina). The troops stayed to protect Saudi Arabia after the first gulf war. It wasn't so much "Islamic governments" as it was the hardline Sunni elements who thought those governments were insufficiently pious/too close to the US.
These groups would also have been pissed off about US support for Israel, but that's not what is being referred to as the US "occupying Muslim Holy lands".
The Islamic Republic of Iran would also have been upset about those issues, but they were not aligned with Sunni militant groups like Al-Quaeda.
It's worth noting that the US troops were deployed near the Persian Gulf and Iraqi border, so not particularly near to the Muslim holy cities.