Al Qaeda (the core part anyway) has never really had an anti-Shia bent (or, interestingly, anti-Israel) and Iran did tolerate some movement of Al Qaeda and Taliban through their territories.
Iran did have a real ally: the Syrian government of Assad. Even that was a difficult relationship prior to the fall of Hussein in Iraq because Assad was a Ba'athist (which is a secular ideology opposed to Iran's theocracy) and Hussein was also Ba'athist (Iraq and Iran were enemies since the Iranian revolution for those who missed that bit).
Ba'athism is pretty much irrelevant today, but until the 1990s it was one of the factors that shaped the Middle Wast we see now.
Edit: I assume the downvotes mean I'm factually incorrect about something. I'd appreciate enlightenment.
(The last I read, ISIS was fighting with all the other rebel groups in Syria? I thought that included AlQ? Also, is that really Saudi policy?! [Saudi A do send weapons to other rebels!] )
(sam88 is a three hours old account.)
(Imams are tightly controlled in places like Iran, Turkey or Egypt. Why ? Well let's put it this way : "mosque" does not mean house of prayer. It means fortress (house of prayer is masjid. Keep in mind that that arabic is weird. Masjid by itself means house of prayer, but combined with other words it means different things, sort of like latin). The states there, well, it's not like there's anyone in them that doesn't know this. So recruitment of locals there cannot easily happen, except by the "state" (which may be a lot more local state than a map would have you believe))
The problem is what western agencies are pointing out, but nobody's listening. Currently Syria and Iraq are the targets. Mostly because they're in the middle east, and allow "other" religions (Shi'a islam is "other" to these guys, as is Druze religion, Alwite, hell, they're not all that fond of wahhabism (too many compromises for the state and the oil, first and foremost of course, the alliance with the United States, and "with Israel") ...). That won't last. We, as in you and me, England and Sri Lanka, Japan and Alaska, are on their list. They're just having some trouble with numbers one and two (Saudi Arabia and Israel).
Al Qaida has/had quite a bit of popular support in Saudi Arabia -- AND the explicit goal to overthrow the Saudi royal family. If you check history, that is what makes you top-of-the-list to most any dictatorial junta!
http://en.wikipedia.org/wiki/Al_Qaeda_in_Saudi_Arabia#Ideolo...
"Like al-Qaeda, it opposes the Al Saud monarchy.[8] AQAP was formed in January 2009 from a merger of al Qaeda's Yemeni and Saudi branches.[1] The Saudi group had been effectively suppressed by the Saudi government, forcing its members to seek sanctuary in Yemen."
I write this because I want to point out:
It is disgustingly dishonest to blame a country for what a dozen individuals do, like you do with the 9/11 terrorists. If we allow that "reasoning", how should the world judge all Muslims considering the millions of murders/rapes/etc in Sudan? (At least those Muslims from the large part of the Muslim world where the criticism about [Sudan's violations of] human rights is ignored or claimed to be a western conspiracy.)