to be worth something (it)– to be valuable, important, useful, special or advantageous enough
to make the cost, risk, effort, disadvantages, pain (needed to get it or keep it or endured after losing it)
seem acceptable or reasonable or of little consequence in comparison
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If you will not the pay the price for something because the item is not worth it,
the quality of the item lessens the actual value of it: the price is too high.
If another person is described as not worth it, the quality of the person (his/her decency, honor, character)
is deemed too poor (of little value) to justify much effort, pain or anything else.
In this sentence, the HE does not deserve the crying person’s emotions, time  or tears.  Losing HIM is not really much of an actual loss.
(He is/was not a truly good person or friend or whatever.)