Just my speculation, but from the article and Tesla's announcement, it looks like this is an availability thing given Tesla's current scale, not a cost thing per se. Ie., they're not worried that commercial users are consuming too much electricity or anything like that, rather the limited resource in question is the actual number of physical spots at a supercharger area, which is a hard thing to scale quickly. Eventually we can expect that electrical car infrastructure will become sufficiently ubiquitous that it won't be an issue, but for now in a still relatively early bootstrapping stage of things I presume that Tesla is concerned that their customers feel as little anxiety or charging irritation as possible. Tesla is most interested in raw numbers of customers (necessary for efficiencies of scale) rather then how hard each customer is using the car, so they want superchargers build out optimized for serving the maximum number of customers regardless of price.

You're right that maybe long term they could set up more to serve commercial capacity on the back of higher commercial prices, but particularly in metro areas acquiring land, permits, and so forth and building physical infrastructure isn't quick.