A couple of questions...
Is Iran holding them prisoner or not?
If not, then why are they playing this kind of game... Al qaeda hates the Shia's and it could get ugly for Iran.
What is your take?
I am presently reading Breakdown by Bill Gertz, which was published in September, 2002. In the book, Gertz states unequivocably that AQ is tightly linked with Iran.
This tension between Shi'a and Sunni is probably overblown. Historically, look at Spain during the Reconquista, the Byzantine Empire during its long decline between Manzikert (1071) and the capture of Constantinople (1453) by Fatih Mehmet II (Ottoman), or the Crusader states in the Levant (1099 to 12xx). In all of these examples, some Muslims would work closely with Christians. Sure, the Sunni may view the Shi'a as heretical and vice-versa. However, the gap between Shi'a and Sunni is much less than the gap between Muslim and Christian.
What is important is how does one advance one's interests. The enemy of my enemy may become my friend.
I think that these arguments that AQ would not work with Shi'a Iran or AQ would not work with secular Iraq are being put forward by people without a whole lot of knowledge on the subject but, having heard a one-line argument, think that they've acquired a deep understanding of 1300+ years of history.
I also note that Iran under the Ayatollahs has long been hostile to Saudi Arabia. AQ and Iran share an interest here, as well.
They hate each other, but remember: THEY HATE US MORE
They may disagree on religion, but they are fellow Muslims to each other.
Remember the Hitler/Stalin Pact, where they agreed to an alliance to carve up Poland.