Glassfish with Apache Frontend

I have deployed web application in Glassfish 3.1.2. I am front ending it with Apache 2.2 and accessing it. I have observed that the access file of Apache .htaccess is not working with Glassfish hosted application though I am accessing it with Apache only. There is no problem with .htaccess file as I tested it with various other hosting. I have copied .htaccess file in document root of Glassfish deployed application. My queries are
1. Does .htaccess comes into the picture when we frontend Apache with Glassfish?If so , what else is required to work it with Glassfish? any setting in Glassfish?
2. What is .htaccess level equivalent availble in Glassfish?
3. How to protect Glassfish from bad bots ,web attacks etc even when it is frontened by Apache?
Thanks in Advance...