Sounds like you're not downloading the files properly. Seems like when you see a link to download a mod you're saving the link rather than following it and looking for the download button?
For files locally stored on SubSim.com here's how to download one.
Lets say we wanted to download ddrgn's No Ship Reflections. We see this link on the mod's release post:
Quote:
Originally Posted by ddrgn
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If you right click on that link and "Save link as..." you'll end up with a downloads.php. This file won't help you at all, it's just the output of that page. You need to follow the link to get to the download page itself.
From that second page, as seen below, just click on the little "zip" icon to download the file. The yellow/blue folder in a vice icon.