I see people linking me to amazon all the time when I ask for book recommendations. Often, I end up buying things as a result of things I see on reddit.
(I don't work for viglinks, but I think the idea behind it is brilliant. As a user, this is the most non-intrusive way to monetize a site I've yet seen.)
For the size of reddit and the potential of the revenue stream, they would do much better signing up to the top X (where X is in the hundreds) affiliate schemes themselves and doing their own re-writing server-side (no lag introduced on the client side).
As a secondary revenue stream, reddit could then make an API available for others to do the same and charge only 15% for the service... undercutting viglink and making more revenue for themselves from other sites.
URL rewriting is easy, and signing up to affiliate schemes takes 30 seconds and is only done once per scheme... there's no reason to give away 25% of revenue for it.
Reddit does a fantastic job of communicating with the users; if they explained what was happening, I think the users would be fine with it.