The PEs of superstores do not reflect the fact that they use much more debt than pure-tech firms. This debt contributes to cash-flows, which contributes to expanding operations. While Amazon may not be able to add new big-box stores with this cash, it can add more ads. Take a look at Amazon's return on equity (of which LT debt is a component) and you will see a brighter picture than depicted in this article.
PE is just one measure, and it is easily distorted in the short-run. Look at the business as it relates to the market price, and then compare it to other like businesses.