What appears to have been the case was that Saddam allowed al qaeda to base in Iraq, but gave them no support

Yea, you can use my country to train terrorist to put the big hurt on the USA because they humiliated me in the Gulf War while trying to establish myself as the supreme ruler of the Middle East and my attempt at assignation of there president failed so you can have a try at the US but we can't show evidence that I'm supporting your group because if it is found out the whole world will come down on me.

Personaly I think Saddam and sons were willing to overlook any differences they had with Al Qeada for the greater goal of confronting and damaging the US.