There is so many ways to hack web sites. Check your error logs. Make sure you have the latest version of PHP, ASP, or whatever server scripting language you are using and the latest database language. If you have any forms on your web site restrict them from entering HTML code and if you are retrieving fields from a database use something like mysql_real_escape_string so they don't do a SQL attack and steal data from your databases.
You might want to pick up a book on how to hack web sites so you can figure out the latest ways to hack web sites (and protect yourself from them). There is web sites where you can practice web site hacking that shows common ways hackers gain access.
www.hackthissite.org for example.
And always back up your web sites so if a hacker ever defaces a logo or erases files you can replace them. I did one web site for a client where they replaced his index.html page with a photo of an American flag burning.