Regular files & folders
In a fresh cPanel hosting account, these are the files and folders you will find by default in your /home/user directory.
/public_html — To make your website publicly available over the Internet, please upload your web pages and images into this folder.
/public_html/cgi-bin — CGI Bin directory.
/public_html — It is used to store the images for any webpages you upload.
/public_ftp — It contains files to be accessible via anonymous FTP.
/public_ftp/incoming — Files uploaded via anonymous FTP.
/mail/ — It stores the mail data.
/mail/new — Stores incoming mail that has not yet been marked as received by IMAP.
/mail/cur — Mail sitting on the server.
/mail/tmp — Temporary directory for mail.
/tmp/ — Temporary files created by cPanel in various activities. Third party scripts may also use this directory for their own temporary files.
/etc — Stores other information related to your website.
Hidden files & folders
/.cpaddons — Stores information about cPanel Add-ons for particular account.
/.trash — Items deleted or moved to trash in cPanel File Manager.
/public_html/.htaccess — The main .htaccess file for the pages served on this cPanel account over HTTP.
Mostly .(dot) files are configuration files for the respective service. e.g .softaculous, .fantasticodata
All the above files are safe to keep or use as you deem fit. You may also want to inspect them to get familiar with them.