For all three of the sports, this is not representative of most of what the average invested long-distance athlete spends or how they interact with the sport. For example, if you run alot you're definitely going through more shoes than 1 pair a year to not risk injury, so increase that to $400-$500 / yr. Set aside $100-$500/yr for races. Don't forget $100-$200/night for the hotels, and a few hundred for travel and food. A good watch to help you improve your training is $400-$700. You don't want to chafe so get good running equipment and keep it up-to-date ($300/yr). When you become competitive, you might want to push yourself further with group training sessions or coaching ($50-500/mo). Your nutrition will be very important when you run far so account for $300-$1000/yr in extra groceries, nutrition items, sports drinks, gels, etc.
Now with just these we're easily over $10K/yr total costs, for just running. I won't even dig into cycling.
I totally agree running is low cost and low barrier to get into. But as you start investing more time in it, joining the local community, participating in races, making friends in the sport, and setting more aggressive goals, you find the costs do go up.
Yes, this is obviously an extreme example, but so was yours. I hope you can see how the average somewhat-invested runner easily spends close to what the article quotes.