Allow Arabs on the train without the security checks on them, if they react positively then continue this way, but if the Arabs become a problem then add security check points. It would be a good idea anyways to place moral security police or IDF soldiers aboard the public transportation, it would prevent racism and hatecrimes onboard, but it must be fair and not partial to the nonArabs. It would also add a sense of security to the people who use the public transportation system to have armed soldiers or police aboard the light rail. Honestly, it's not only Jews who need protection from Arabs but Arabs need protection from wicked Jews too, thus what I meant by "moral" security agents.
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from the article: Officials slam 'racist' Jerusalem light rail survey