Just wanted to say a big Thank You and report that this helped me too, after lots of searching and trying Stack Overflow and many other sites, this one post led me the right way.
Upgrading from Apache 2.2 to 2.4 and moving to suphp handler, I started getting the "no input file specified" response for URLs hitting my RewriteRule rules, for example:
RewriteRule ^/rma_agreement /index.php?main_page=rma_agreement [QSA,L]
was designed to pass the user through from the /rma_agreement url, with all query parameters intact, to a rewritten URL for the Zen Cart system. It failed when run on Apache 2.4 using suphp. Changing this to:
RewriteRule ^/rma_agreement /index.php?main_page=rma_agreement [PT,QSA]
makes it work again. I don't know enough about the rewrite pipeline and cgi or suphp to know what was failing or why PT makes it work, but it works and that's good enough for me! Hope this helps others in future.