I have an existing wordpress site with a magento instance in a subfolder named /shop. When I type in my address and add /shop to the domain it just routes back to the wordpress site. However when I had an index.html to the magento instance it serves up my test content. Is that in htaccess? I just want to add a store to an existing blog site.
Change the RewriteBase line in the Magento htaccess to be /shop. The line will default to / and be commented out.
Let me know if that works for you.