You are using Automapper incorrectly, you need to use the QueryableExtensions namespace, so your code should be
IQueryable<Company> companies = CompaniesService.FindCompanies();
CompanyListItem[] results = companies.Project().To<CompanyListItem>().ToArray();
Also if you where going to do it the other way you still had Mapper.Map
wrong, it should have been
IQueryable<Company> companies = CompaniesService.FindCompanies();
CompanyListItem[] result = Mapper.Map<IEnumerable<Company>,CompanyListItem[]>(companies);
but I still recommend doing the .Project().To<T>()
method as it will perform the mapping server side instead of client side so you potentially have less data that needs to be sent over the wire.