Interlinking is definitely a factor - but content is what matters.
Take the Disney brands that live on Go.com:
They all live on Go.com but Google surely knows they are really separate sites that cover different topics. Same for any blogspot.com, typepad.com, etc. hosted blog. The millions of blogs there cover a wide range of topics and search engines understand that they are not related just because they share the same host domain.
On the other end of the spectrum - if your site just has two subdomains - let's say www.website.com and blog.website.com ... which cover the same topics and link to one another, search engines would more likely associate those two addresses.
