I wear rubber boots but I also spray some pine cover scent on them. New rubber boots tend to have a stronger rubber smell to them at first but I have never noticed that to be a problem. Deer do smell the rubber but it has never alerted them from what Ive seen . Deer dont seem to get alarmed at all by the rubber.
If I were you I would wash the new boots thoroughly in a scent free detergent and just keep them clean from then on. Using a cover scent like pine or acorn wouldnt hurt either.