I've noticed for years that if you click a link from the main Forum page you go directly to the source site. If you click the link in the article page you go to the FR redirect page and then to the site you wanted. Maybe FR’s redirect page is the problem.
It is the redirect page that is doing it, Google has tightened the malware warnings. Here's the thought process: User clicks on link to go to page on freerepublic.com, gets to the page and immediately, it tries to load up another page on a completely unrelated domain. The warning being: Hey! You're not going to the page you wanted to on freerepublic.com, they're trying to send you to cnn.com!
I'm not sure how important that redirect page is, other than a fixed source page so that if anyone asks, it can be shown how many times people clicked through to an article from a story and to mask exactly what story page they came from. Since the front page links don't go to the re-direct page (why should it, it just shows the main forum page?) there's no warning, as you intentionally chose to use a link to another website.