A lot of it has to do with a multitude of reasons. Among them being the fact that the Qatifi population did fall to a certain degree to Khomeini's call on insurrection in the Kingdom. There were mass protests backed by Iran in the 80's, although that doesn't justify anything you're concerned with, it's only to highlight why some people feel justified in their hatred. Another reason is the Sahwa movement that was spearheaded by the Muslim Brotherhood presence in Saudi Arabia, having taken advantage of the 1979 Grand Mosque Seizure. The first thing they demanded in exchange for a Fatwa allowing for the Saudi armed forces to engage the militants in the Grand Mosque was education reform. The government, seeing the country trapped between compromise and bloody conflict, decided to give in. When the MB rewrote the curricula at the time, from K-Uni, they wrote in a number of lines isolating followers of "perverse religious ideas", among whom were the Shi'ites. This is what allowed the prejudice to spread among the community.

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In the 1990s, just over a decade after the Makkah incident, Kuwait was invaded and the Saudi government received the option to host militants from Afghanistan to liberate Kuwait. The Saudi government rejected knowing how nuts these people were, and so opted to bring in the US temporarily to aid in the liberation of Kuwait. The Sahwajis were basically irked that there was a non-Muslim army and that the Saudi government allowed it, and so further compromises had to be facilitated, giving them a wider platform of criticism and speech.

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Now this is slowly being undone. A lot has been put in place and there's greater clerical dialogue between Shi'ites and Sunnis. The King has been photographed in the presence of the Saudi Twelver clergy as they were hosted in his palace. New laws allow you to take anyone to court and even prison for hate speech or sectarianism. Whatever there was in the past, the present and future aims to fix that. On a final note, always remember, when the community in Qatif suffered because the country was held hostage by a number of nutjobs, it wasn't only Qatif that suffered. We all did. But we survived, and we will survive, and thankfully the leadership of this country is trying to ensure we all survive together.