Site security

[Jam Man]

I received an email from Google a few days ago telling me that my site had been compromised. I didn't see any malware when accessing directly, but only realised that my site was being redirected to a malware site via search results. I deleted the .htaccess file that was responsible for this and put in place an old backup for the time being. I've now checked again and can see users get access to site via search as they should. 

I just want to know how I can protect the .htaccess file from being compromised in future. This has been a one off event over 4-5 years so don't consider the site vulnerable as such. But I'd like to know how to prevent something like this happening.

[MADMAN32395]

What version of ips ya on? Is it outta date? Missing security patches?