First, WD-40 is not a lubricant. It is a solvent. Use some silicone grease or white lithium grease to lube up the sections of the antenna when it is extended. Then cycle it a couple times. Hopefully, that'll do it.

But if the rumbling noise continues, my next guess is the slipper clutch on the gear that drives the antenna up and down.

On the 94-01 Integra, there is a threaded nut on the antenna motor casing that allows you to tighten the clutch. You have to dismantle the interior of the trunk to get to it, but it's a fairly quick job.