I worked for Costco so allow me to enlighten you.
Costco carries about 3500 SKU's total and has limited space. Their profit margin is incredibly small.
They run by the numbers. They have to or they will go broke.
Costco is not a bookstore. It simply sells some books along with all it's other offerings.
It has a responsibility to its shareholders and their very highly paid employees.
If Dinesh D'Souza's book is not meeting the numbers, it has to go.
They carry (IMO) a higher number of conservative books over liberal books because conservative books sell better.
It's as simple as that.
From Costco's Facebook page:
Dear Costco Members - Costco does not make purchasing decisions based on personal or political leanings. Each item we carry must meet sales thresholds in order for us to continue to stock them.
We purchased this item with the best intentions when it came out on June 2nd, unfortunately it was not meeting the necessary thresholds and was a part of our normal weekly returns effective July 1, 2014. - Karen