There have been anarchist unions and many anarchists are union members. Anarcho-syndicalism is a flavor of anarchism based off unions. IWW is the most obvious example. Anarchists would all have a problem with the popular modern union for sure, with top down structure and how they are beholden to political parties but it doesn't mean if that is the only option we should just refuse to support it. Like dandays said above having workers organized is always better than not because the organized workers will always be able to demand more "fair" wages, work rules, etc.
Decent article about anarchism and unions. http://anarchism.pageabode.com/anarcho/there-is-power-in-union