The lower-tier Prius' are profoundly less expensive than even the mythical base-model Model 3 (which the article points out, isn't available; Tesla has said they hope to offer the base model by the end of the year). A 2017/2018 Toyota Prius can be driven off the lot for $20,000. The Model 3s that have been sold are $40,000+. That makes A Prius Prime plug-in hybrid the most direct competitor. I trust the sales figures quoted are accurate.
But there's more to it: Price, availability, utility, and maintainability are big considerations once you leave the ultra-luxury price range (100k+) that is Tesla's core market. The Toyota wins in all these aspects, in my opinion. Where Toyota does not compete is the "status symbol" market.