Issues after hack cleanup

I have several WordPress sites on a shared hosting account. They were all hacked, and I decided to more or less start over. The problem I am running into is that after I have installed WordPress to either the root of public_html or a sub directory (it doesn’t matter which) going to any of the index.php pages shows the “Index of/” directory listing instead of the page. If I navigate to login, it gives me the login page, and after I login if go to /wp-admin/post.php for example, that works too.

I think the problem lies in the .htaccess file(s) but I am not sure how to fix it. I did some Googling and tried creating a .htaccess file and placing it in the root per the instructions here but that was only partially successful.

I wasn’t able to salvage the original .htaccess files; they were hacked too. On a side note, I am also researching security and hardening best practices to try to avoid this in the future.