Explain and complain. Some book stores are not really aware they they stock anti-Catholic materials or do not have a strong commitment to carrying it, and pointing it out can get it taken off the shelves. The best thing is to approach the cashier and ask to see the manager (or assistant manager if the manager is not there). This will be the person who makes the decisions. In talking to the manager, stress three things:
First, stress the orthodoxy of the Catholic Church, citing examples of things that the manager will consider foundations of orthodoxy (e.g., the Trinity, the fact we are saved by grace and do not earn our place in heaven, that we must all repent of our sins and have a "personal relationship" with Christ).
Second, stress errors in the anti-Catholic material. Even if the manager doesn't mind carrying anti-Catholic material, he may mind carrying erroneous material.
Third, stress the hatefulness and divisiveness of the mind-set which motivated the production of the work.
Finally, give the manager something to read about the anti-Catholic material (e.g., This Rock's article on Dave Hunt's A Woman Rides the Beast or Christianity Today's exposé of Alberto Rivera).