Yes - it's the use of pesticides by cotton growers that have people up in arms about the product. Also that hexane is used in the distillation process- but many other oils are processed this way. It also has a short shelf life and can be prone to rancidity and DOS. Used in small amounts that shouldn't be an issue.
Cottonseed boosts your lathering properties in soap.
You'll have to do your research as far as the pesticides. Some think its hysteria. The oil itself is regulated as a food oil and would have to meet the same standards that Soybean oil meets - which also is known to be grown with high pesticide usage. No one is picking on soy!
I think it's safe to say that there is a bit of a snob factor to calculate into the equation as well. Even with customers. Soaps with soybean and cottonseed oils listed on the ingredients list will be perceived quite differently than soaps with Crisco on the label even though it's the same thing.