No one likes it when they get malware on their computers due to an infected site. So that is why Google tries to warn searchers when a site may have malware on it. But Google tries to be as specific as possible, when it comes to malware warnings.

In fact, when possible, Google will report malware issues on subdomains or subfolders only and leave the root domain alone. JohnMu of Google said in a Google Webmaster Help discussion thread:

That is why a specific blogspot.com blog can be reported as having malware, whereas the main domain will be safe.

Forum discussion at Google Webmaster Help.