Right now, it seems your choices are to have CyberDuck copy the permissions from previous files, or else apply a user-definable (but fixed) set of permissions for upload and download.
I'd like to apply defined permissions based on what kind of file it is: at least, one kind for folders and another for files; and preferably also different permissions for different kinds of files -- .html, .gif, .htaccess, etc. In fact, it makes no sense to apply the same permissions to folders (which most commonly you'd want to be executable but not readable) and files (which are normally the opposite of that).
Is there some way to set more fine-grained permission preferences in CyberDuck that I don't know about? If not, I'll try to submit it as a feature request, if I can figure out how to do that.
Thanks,
Jonas