Many hacks are caused by out of date or insecure software. Also if your webpages displaying virus, then We would advise that you do the following to prevent this in the future:
As this is an isolate incident with only your account (There isn't any possibility to hack / Virus attack to the server) it is an issue within your account that allowed access.
1) Clean all infected files in your account and remove any unknown/un-needed files. (It is better to Remove all files if possible)
2) Change all passwords including cPanel, and FTP to STRONG Passwords ( https://www.microsoft.com/protect/fraud/passwords/checker.aspx )
3) Scan your computer for viruses (Using uptodate Good virus guard) , some exploits are caused by a virus on your computer getting your login and uploading files. Also scan your PC for any spyware.
4) Update all applications on your account and remove any insecure plugins / widgets (Some insecure widgets / plugins on WP / Joomla / Forums .... )
*** We strongly advice you to check your HTML page coding for any iFrame (Normally bottom of the page) tags and if found remove those.
5) Finally you can upload your fresh files to server account. Also remember you have to use strong Passwords to All site software (Eg: open source / scripts...)
Find the strength of your password here >> http://www.passwordmeter.com/
