Nike 2014 net profit margin: 9.69%
Footlocker 2013 net profit margin: 6.59%
The answer: neither is making THAT much on a per shoe basis. If Nike sold them directly to you at $97, it would be breaking even on a net basis. For Footlocker to do the same, it would be $107. Note that this does include expenses not directly tied to the making of that shoe (or in FL's case, the selling of the shoe), but realistically if Nike was not spending what it was on R&D, well, it wouldn't be Nike would it... (and FL has overhead it has to cover as well).
Shoes cost what they cost. They basically did not change in price at all from 2007 through 2013 due to the bad economy (prices are sticky on the downside, thus why they stayed where they were rather than dropping under $100), but now that things are improving, the companies are (quite reasonably) beginning to make up for the lost inflation.