You have misunderstood; SpaceX obviously doesn't have a profit margin of 99%. The 100x comparison was with the space shuttle.

Then it really shouldn't have been written immediately after "Wait, that's price. SpaceX is profitable." The two statements have literally nothing to do with one another and it's easy to see why one would assume that the final sentence is talking about the sentence immediately before it.

The implication to me and others was “it’s roughly 100x cheaper than the (3k/kg) price”

And that wouldn’t be a profit margin of 99%, it would be a profit margin around 10000%