By default, when you use the File Manager in cPanel, it does not show hidden files. Hidden files are any file that begins with a dot, such as .htaccess. .htaccess is actually a common file to edit, and so if you would like to edit the file using your File Manager, you'll need to ensure you have the option selected to show hidden files.

Showing hidden files in File Manager

Step 1: Log in to your cPanel
Step 2: Under Files click File Manager
Step 3: Click Settings in the upper right corner
Step 4: Select your Document Root and check the box for Show hidden files and click Save