Actually that business model works pretty well for someone like Nike, who has announced they expect their DTC business to increase dramatically over the next few years. I'm glad you mentioned the Nike Free, because I would argue that the typical "Nike Free customer" is not a running store customer. They may not be a runner at all. The "Nike Free customer" wasn't necessarily recommended that shoe, but they put it on because it looked cool and felt light and maybe they even had it just to wear casually but decided to try it for going to the gym or running. They figure it must be a great running shoe because they assume Nike is the best, and that's because they're the biggest, coolest brand. The "Nike Free customer" doesn't need to go to a running store because they already know they want that shoe and everything else doesn't have a swoosh on it. Plus, they can order it online in a dozen different colors or even create their own, and since color and style are very important details to this customer, why bother going to a store that will likely be unable to carry every option? Nike doesn't care about little local running shops anymore, they just want to pump millions of these out to as many purchasers as possible.
On the other hand, people are more likely to go to running shops when they don't know what they want. Or maybe they have some idea, but they want to experiment with their options. This type of customer is usually looking for what works rather than being blinded by brand name and might be willing to try something they've never even heard of, especially if the comfort blows them away. It seems like you have a bad impression of running shops and I know they aren't all created equally. It's true some running stores favor the "easy sale" but many emphasize spending time with the customer and building relationships as far more important. They shouldn't be biased towards any certain brand, which means every shoe on the wall has a chance. If your product is worthy it will sell.
Big names like Brooks and ASICS still lead the market but that doesn't mean that the new guys don't have a chance. Golden Harper of Altra and Tony Post of Topo both personally visited countless running stores and managed to get their new, unusual brands on many shoe walls. The growth for Altra, while aided by online advertising, has been ridiculous. However, I understand that getting into stores is very difficult and costly. Skora came about during a time when every established brand plus an equal number of new companies were promoting their own "minimalist" footwear. Since then, the category hasn't become the major market share monster some expected. That's certainly working against it. Perhaps online only truly is the best option for you. However, I wonder how long it will be sustainable.