... not to hijack the thread, but I'm of the camp of believers that advises NOT to use silicone for a window/door/fan install!
Here's why: Just try taking that stuff off in five years. Just try. Use mineral spirits, WD-40, soap and water, whatever. Even when you think you've got it all gone, residue will still be there. No solvent dissolves silicone, and the residue will prevent the next sealant (silicone or otherwise) from properly adhering to the substrate. You have to tackle the thing with a metal abrasive pad. Basically, silicone is only recommended for permanent waterproofing, not for seasonal applications. At least that's the reigning theory.
Dicor, Geocell and other RV parts suppliers manufacture specific non-leveling sealants designed for this exact application. I use Geocell Pro Flex. Might not be the best, but so far it's great! Goes on easy, sets up in minutes, easy to clean up with mineral spirits, and lasts a lot longer than silicone.
If you line the flange of the fan with putty/butyl tape and then seal with Pro Flex or other sealant, you'll be fine. I'd wait 10-15 minutes after you first install the fan (with putty tape and screws) to apply the sealant. Gives time for the air bubbles to escape.
Last but not least ... some people use roofing repair tape, like EternaBond AlumiBond. Personally, that seems like overkill, but if you're really worried and want to be able to drive through a hurricane and stay dry - that stuff works!

Good luck!