Your website may rank one of the top websites and you may have done a good job in applying security best practices, however, it gets blacklisted by some tool such as Google Safe Browsing. Although your website is not malicious by nature, it may have been hijacked. Google Safe Browsing is the most popular security blacklist in use. This tool is used by Firefox, Safari and Google Chrome and users of these three browsers are warned not to visit your site plus Google puts warnings in their search results. To use Google’s tool from any browser, you can append a URL to the end of http://www.google.com/safebrowsing/diagnostic?site=.
Read more here – http://research.zscaler.com/2012/05/look-at-top-websites-blacklisted.html