If you build Fluent from source, there is now support for filters. You use them like this:
First create a class inheriting from FluentNHibernate.Mapping.FilterDefinition:
using FluentNHibernate.Mapping;
namespace PonyApp.FluentFilters
{
    public class PonyConditionFilter : FilterDefinition
    {
        public PonyConditionFilter()
        {
            WithName("PonyConditionFilter")
                .AddParameter("condition",NHibernate.NHibernateUtil.String);
        }
    }
}
In your ClassMap for your class, use the ApplyFilter method:
namespace PonyApp.Entities.Mappings
{
    public class PonyMap : ClassMap<Pony>
    {
        public PonyMap()
        {
            Id(x => x.Id);
            Map(x => x.PonyName);
            Map(x => x.PonyColor);
            Map(x => x.PonyCondition);
            ApplyFilter<PonyConditionFilter>("PonyCondition = :condition");
        }
    }
}
Then add the filter to your fluent config:
Fluently.Configure()
    .Mappings(m => m.FluentMappings.Add(typeof(PonyConditionFilter)))
    //blah blah bunches of other important stuff left out
    .BuildSessionFactory();
Then you can turn it on and off just as you would with vanilla NHibernate:
session.EnableFilter("PonyConditionFilter").SetParameter("condition","Wonderful");