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
Log into your cPanel
Click the "File Manager" icon
Ensure "Show Hidden Files" is selected