configuration.cs

var cfg = new Configuration()
    .DataBaseIntegration(db => {
        db.ConnectionStringName = "MyConnection";
        db.Dialect<MsSql2008Dialect>();
        db.Driver<ProfiledSql2008ClientDriver>();
    });

ProfiledSql2008ClientDriver.cs

using System.Data;
using System.Data.Common;
using MvcMiniProfiler;
using MvcMiniProfiler.Data;
using NHibernate.Driver;

namespace MyProject.Infrastructure
{
    public class ProfiledSql2008ClientDriver : Sql2008ClientDriver
    {
        public override IDbCommand CreateCommand()
        {
            return new ProfiledDbCommand(
                base.CreateCommand() as DbCommand, 
                null,
                MiniProfiler.Current);
        }

        public override IDbConnection CreateConnection()
        {
            return ProfiledDbConnection.Get(
                base.CreateConnection() as DbConnection, 
                MiniProfiler.Current);
        }
    }
}