Auto-upgrading WordPress and the .htaccess file

A pattern I have observed in the past months:
A couple of days after auto-upgrading WordPress, access to the WordPress blog is blocked.

My non-programmer’s workaround is:

• Rename the .htaccess file on the WP level. The WordPress blog displays.
• Login and go to Settings > Permalinks and re-save settings, or copy old .htaccess file content and upload by FTP to the server.

I would like to understand why this happens. Immediately after upgrading the WP install, there are no visible problems… but 2 -3 days later I come home to see that my site is down.