Malware infection is very prevalent these days. But one can take a few steps which prevent malware infection on your PC and in turn on your website. Most basic but important of these steps are :

1. First step is to avoid Internet Explorer browser at all cost for browsing, as it is the most common entry point for all malware. One can easily download Mozilla Firefox, Google Chrome etc and make it the default browser.
2. A good antivirus like AVG always helps, even its free edition automatically updates daily.
3. Ftp/cPanel passwords should be changed very regularly, its as important as changing your ATM pin number.
4. Use cPanel 'File Manager' or other control panel File Manager : We recommend uploading of content via cPanel File Manager, as it has now become very user-friendly and easy to use. Modifying content of your website via File Manager is most convenient now as its just a right click away. Multiple files can be uploaded via zip file and they can be extracted in realtime on the server.
5. Get a LIVE Ubuntu CD. One can download CD image of Ubuntu from http://ubuntu.com and burn it. Through it, one can easily access internet and update and upload files, without installing anything.

Certainly there is much more to it, and I will be posting it every now and then, do check back later.