Securely access them in what way, are you referring to encryption or limiting the users access?
If you want to force encryption, you can do so for FTP as well using FTPS
In WHM go to
- Home »
- Service Configuration »
- FTP Server Configuration
and set "TLS Encryption Support" to Required.
If you are referring to limiting an FTP user access to a specific directory, like public_html, then you can create them an FTP in cPanel as well as specify the home directory so if you do public_html they will not be able to browse the home directory of the account.