I wanted to post this because I saw quite a few people having the problem that I was having. I managed to find one thing that caused my problem, as opposed to disabling this plugin or that plugin, none of which I had installed.

The problem:
When changing the default permalink configuration from ?p=5 to /2013/05/my-cool-post, all of a sudden the links to both the posts themselves and to the comment buttons were giving 404 errors. After much searching.

Supporting Evidence:
Some people reported having multiple sites hosted in the same wordpress account or hosting account, but only having this problem with 1 site. This tells me that it is specific to the site, not the hosting provider, or even WordPress. That’s what led me to the solution.

The solution:
While perusing through the httpd.conf file on my system, I was looking at the following:

<Directory />
    Options Indexes FollowSymLinks Includes +ExecCGI
    AllowOverride None
</Directory>

Notice that “AllowOverride None” is set, which basically disables mod_rewrite (an apache module necessary for WordPress to be able to rewrite your urls — ie use Permalinks). I changed this to “All”, and restarted httpd, but still had the same issue.

Finally I went through and searched for “Directory”, and there are quite a few of them in there, but then I found another stanza:

<Directory "/var/www/html">

With quite a few comments inside of it. (That’s why I didn’t notice it the first time around.) Inside that Directory stanza, was this:

AllowOverride None

This one was overriding the “/” directive earlier, so as soon as I changed this from “None” to “All”, and restarted httpd, my links worked perfectly afterward.

I hope this helps you guys, it seems to be a chronic problem in WordPress.