When chromes give you warnings like that on sites that you know are legit (i.e. this one) its probably just a bug.
Not really true. One of the most popular malware checks for popular FTP programs that are installed, and if passwords are stored, it will use those FTP connections/passwords to log in and alter files on the server, injecting malicious code into "legitimate" sites. The only way a normal user would notice is if their AV software catches it, they're using NoScript, or the browser has some built-in protection. Based on that message, it looked like that or something similar happened to AP.net (but everything looks fine now).