Understanding of the command line, delayed WYSIWYG feedback loop, FTPing/synchronizing files. Some generators don't even tackle "pretty, easy to install templates a la Wordpress" either.
All surmountable, but I haven't seen an "all in one, easy to use" fix yet.
I'd love if I could recommend a single client-side app for people to use that did it all. Something like Coda but tailored for beginners?
Frankly, I'm not sure it matters. Give the average user a CMS with a WYSIWYG editor and you soon end up with a hodgepodge of fonts, sizes, eye-jarring colors, general inconsistency, and 2MB images rendered as 48x48 icons.