Okay, first of all, something needs to be made clear here:
You do not have a "PHPlist site". You have a list management software. No part of that software resides in /public_html.
There is no "site" for anyone to see. The part of this software that anyone can see from the web, consists ONLY of the list management interfaces.
No one ever goes to your "phplist site". They go to the subscribe pages, they go to the preferences pages - but they NEVER go to /public_html for anything unless you decide to construct something there yourself.
Nor do you, as the admin, ever need to go to /public_html.
You manage your lists by going to:
http://yourdomain/phplist/public_html/lists/admin
You don't need an index.html in the public_html directory - in fact, you really should have a 404 "Nothing to see here, move along" page in that directory.
Now, the phplist programmers have kindly dumped an index.html page into that directory. This is a normal and simple security precaution. If your web server is configured to allow "directory browsing" then if there is no index.html, then anyone can see the raw directories and files.
You really don't want anyone browsing around and perhaps seeing your config file and copping your database password do you?
No, you don't.
So, either make sure that the directory browsing is turned off in your web server, or make sure you have 404 pages in all the places where no one ever needs to go (like /phplist/public_html/).
In the meantime, the phplist programmers have added files here and there to stop people from browsing your dirs. Feel free to change those files at any time, but if you don't - you're still covered.