Yes, I go to domain.com to access my wordpress install but all the code is in domain.com/wordpress. I know you can do this with a single install http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory, but I guess I shouldn't have done this with multisite. I installed multisite back in August. As far as I can remember I've always had this redirect problem, but since I could get around it by refreshing a few times I foolishly thought it would go away at some point.
When I go to domain.com to access the main site, I have no problems with redirects. I access my other sites at: domain.com/site1 and domain.com/site, and that's when I get the "too many redirects" error.
Last night I copied everything from the domain.com/wordpress directory to the domain.com/directory. Also, both .htaccess and wp-config seemed to be configured properly for access at domain.com. I also changed the DocumentRoot to use the domain.com directory. I checked the database and while there are references to the domain.com/wordpress path, most were for images and comments (so those broke), but nothing related to the actual path.
And even with this, I would still get the redirect error. I'm pretty stuck at this point...