Hmm, it looks like you're set up ok to me. Do you know where these hits are coming from? It may be a search engine that sees a url like [url=http://www.mikeodom.name/index.php/links/2006/10/09/biker_and_motorcycle_lawyer_blog]this[/url] and thinks that index.php is a folder, so it looks for a file in that folder called index.php. I've never noticed this on my site, but I've never looked for it either.

Thanks for the reply. I noticed the hits to 404 pages shown in my error page stats on my awstats. It showed over 4,000 hits to this link.

404 Document Not Found 5340 83.9 % 1.92 MB
then when I click on the 404 it indicates the offending link:
/index.php/index.php 4289 -
Seems like an awful large amount of 404 error traffic.