Can a trademark registered in India protect my website?

Web domains are basically first come first serve. The primary exception is where an entity registers a domain based on a trademark that it knows is owned by someone else (i.e., cybersquatting). If you are running a legitimate business or otherwise actively using your website, they likely can't do anything to take it from you. This is particularly the case if your use of the trademark in India predates their use in whatever other country.