Larger mods are generally not uploaded to CFC directly. They are simply too large for that, and CFC is not a file hosting provider.
So most mods are hosted on outside hosting services. The issue is mostly that some developers chose to upload their mods to services that turned out not to be permanent, or those that are still around degraded into adware/malware ridden websites. That is the eternal problem of the internet: nothing is as enduring as it seems. Some of these issues exist because the original developers are long gone and have essentially abandoned their mods, so there is nobody around to migrate the content. CFC has lost a lot of assets when megaupload went down, for example.
Personally I try to pick hosting services that look stable, but the Venn diagram with those that are free is small (personally I am using Sourceforge, but they aren't guaranteed to be around forever either).
The best thing I can do to help out is: please, if you have a mod on your hard drive and notice that its download location is broken or difficult to access, please upload the mod somewhere else. Then I can go into the CFC database and update the link to the new location.