When you floss, you help prevent your gums from becoming inflamed. That's a good thing. What is happening when your gums are inflamed is that you have a chronic bacterial infection in your mouth. This harms your arteries through two mechanisms: the bacteria find their way in to your arteries and hang out (causing plaques), and your body mounts an immune response to the bacteria in your mouth, causing inflammation (which in turn can cause your arteries to narrow). This makes it hard for your heart to do its job and can lead to heart disease.
There is some debate about how many years you can gain with heart disease. Dr. Perls says 1.5 years, while Dr. Roizen says 6 years.
I haven't read the studies, but could it be that people who have the discipline to floss regularly also have other good habits?