Frequently I encounter French people who use "que" on its own.

Do you mean something like this:

Que tu passes des merveilleuses vacances. -- Have a great vacation!

Literally: that you may pass great holidays. 

Here you can pretend that the first part of the main clause was omitted. It may be something like: Je te souhaite, ...

-- Chris. 

No I meant that I often encounter the use of que without the preceding ne to mean only

Indeed

I hear that a lot too, especially among French millenials, who also frequently omit the subject pronoun. One hears "vendent que des fleurs" meaning "they sell flowers only". It seems there is a tendency to italianize or hispanize French by omitting subject pronouns where the context is clear. Oy veh!