Yes, standard FTP sends everything over an unencrypted connection so security-wise SFTP would be much better. But many people upload the web pages directly from dreamweaver, frontpage and what not that doesn't support SFTP (last I checked). Because of that many hosting companies stick with FTP because it's old and accepted.
APR could be
http://apr.apache.org/ but I don't see what a programming library has to do with anything. But HTTPS is also encrypted so I don't see why you can't use that other than it might be inconvenient. Otherwise, unless you have an ssh account on your hosting company, I don't think there is much else you can do.