It has nothing to do with religion actually...the system is totally based on bumiputera ....meaning child of the soil which is the Malay constitutes of 7 tribes if you wish...
Which goes back to support my point. They have a racial preferential treatment. A system that effectively places some 40-45% of their country as second class citizens.
Trust me dude, i've been to Kuala Lumpur and have friends who are Chinese Malaysians. They are very vocal about this system; and are against it. This is the reason a lot of Chinese Malaysians leave Malaysia for say.. Singapore or the west.