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How do I learn which particles go with which transitive verbs since it is not always を。
For example:
ラップをかける ラップを被せる
...is no problem, but...
ラップで包む 役に立てる
JDICT says these are all transitive verbs but the last two examples don't take を so do you just learn them as exceptions or set phrases?
You are wrong. They do take を.
ラップでごはんを包む
知識を役に立てる
One tricky thing is that, 知識を役に立てる is derived from 知識が役に立つ, and the reason 知識 takes を in the former is not because it is the (underlying) direct object, but because of what is technically called exceptional case marking.
As for how to learn them, that is too vague a question here.
An ironical question
How do I learn which particles go with which phrase? Why is the truck takes on in:
load hay on the truck
but accusative case in:
load the truck with hay
I've been finding intransitive verbs where reliable sources say they are becoming transitive i.e. the Japanese are often using を to mark a direct object. 触る (さわる, to touch) is my most recent example. It is not always clear from these sources if this is due to a recognized language shift, or just a common mistake.
をthe object is implied. For example, inラップで包むI have no idea what you are wrapping.