In order to understand this, one needs to understand the history and the roots of al-Qaeda.
In the 1920's and 1930's a group was formed in Egypt known as the "Ikhwaan al Muslimeen".
The founder of this group was Hasan al-Banna, who was a Soofee of the Hassaffiyyah Shaadhilliyyah tareeqah, came up with this principle:
نجتمع فيما اتفقنا عليه ويعذر بعضنا بعضاً فيما اختلفنا فيه
((We unite upon that which we agree and forgive each other with what we differ upon)) (Majmoo' Rasaa'il on page 453)
So based upon this principle, this group united with every sect and group without correcting their beliefs or speaking about Tawheed and Sunnah.
Then came Sayyid Qutb, who at first apostated from Islaam for 11 years and went to the west. He was a part of the Marxist group Hizbul Wafd and he followed and Marxist ideologies and the theories of Alexis Carell (particularly the theory of Barbarism which he plagiarized)
He was merely a literary author who had memorized the Qur'aan at a young age. When he was in the west he found the situation of the west despicable so he returned to Egypt and began to speak. He took some of the ideas of Alexis Carell and Karl Marx and he also took the ideologies of Sayyid Abu A'laa al Mawdoodi who was very partial to the Rawaafidh Shee'ah. In fact Mawdoodi used to praise the Iraanian revolution.
Sayyid Qutb wrote books with very corrupt ideologies. One of the key ideologies which he spread was the issue of Takfeer. Sayyid Qutb made Takfeer of the Muslim Ummah by saying that they reverted back to the period of Jaahiliyyah (aka, barbarism... that was the theory of Alexis Carrel verbatim that mankind has reverted to barbarism)
Eventually Sayyid Qutb was executed by the government. It is imperative to note that Jamaal Abdel Naaser, Anwar Sadat and Husni Mubaarak were all members of the Ikwhaan al Muslimeen. Ayman az-Zawaahiree was an ardent admirer of Sayyid Qutb during his youth. After the execution, Ayman az-Zawaahiree formed a radical group bent on overthrowing the government. He was eventually imprisoned.
During the time of persecution in Egypt due to the constant rebellions by the Ikhwaan al Muslimeen, the Saudi government allowed refuge for members of the Ikhwaan al Muslimeen and had allowed them jobs and citizenship in Saudi Arabia out of kindness for the Muslims. (They did the same for Palestinians). This brought in Muhammad Qutb, Sayyid Qutbs brother. Muhammad Qutb took up a position of teaching at the universities in Saudi Arabia. He spread the ideologies of his brother in Saudi Arabia, and soon the spread of the Ikhwaani ideology in Saudi Arabia increased.
A young Usaamah bin Laaden, ignorant and playful used to listen to these Ikhwaanis and take from them rather than attend the Duroos given by the Ulemaa in Saudia.
During this time, the lesser dangerous Ikhwaanis such as Abdullaah Azzaam were preparing for war in Afghaanistaan. When the war in Afghaanistaan erupted with the Soviets, the scholars declared it a Jihaad, and the Muslim governments declared it a Jihaad.
So many Arab fighters went. Egypt sent its prisoners to fight in hopes that they'll get killed. Amongst them was Ayman az-Zawaahiree. But what Egypt did not bank on, was that most of the Arab fighters would not fight much of the war.
During this time the Taaliban were not corrupted in their 'Aqeedah and their ways. Shaykh Jameel ar-Rahmaan was leading the Afghaanis against the Soviets. However some groups of Afghaanis (soofees) were severely against the Shaykh due to him being a Salafee.
The extremely wealthy Usaamah bin Laaden traveled to fight. He teamed up with Abdullaah Azzaam and faced a few skirmishes. His corrupt mindset was not met by Abdullaah Azzaam, when he was approached by Ayman az-Zawaahiree. Given the promise of being the Khaleefah, he joined with Zawaahiree and denounced Azzaam.
During the war, some of these people would claim: "Kill the wahhaabis before you kill the communists"
Some brothers of ours who fought in that war met people like Zawaahiree and said that the way they dealt with the Salafee Muslims was murderous. If you disagreed with anything, they'd kill you on the grounds of you being a "traitor".
After Shaykh Jameel ar-Rahmaan won the war. A group of the deviants from amongst the Afghaanis plotted his death. Amongst them was Hikmatyaar. They slaughtered the Shaykh and spread their corrupt ideology and thereby Afghaanistaan was corrupted.
Then "mysteriously" Abdullaah Azzaam was also murdered and what was left in Afghaanistaan was the corruption of the Taalibaan Soofees and the Khawaarij "al-Qaeda".
This is just a quick summary.
Fighting the Rawaafidh doesn't serve much interest to the Khawaarij over Saudi Arabia and the salafees because frankly the Rawaafidh are a joke. They serve very little threat ideologically towards the Khawaarij. But the Salafees pose the biggest threat because of their strong adherence to the Sunnah, and their refutation of the claims of the Khawaarij.
This is why you find the people upon truth are fought so heavily by the deviant groups. The Rawaafidh HATE Shaykhul Islaam Ibn Taymiyyah because he destroyed their 'aqeedah in his Minhaaj as Sunnah. They HATE Shaykh Muhammad bin Abdul Wahhaab because not only did he ideologically destroy them, but he leveled their center of Shirk Karbalah.
I have more to say but space is limited.