There is no problem with doing that. You might have to solder wires to each wire to extend them, but really you're only dealing with about a dozen wires, it'll only take a few minutes to solder them together.
What type of HU do you have? Is it aftermarket? Do you already have a wiring harness for it? Just make sure that you use good quality wire for the job. You can easily get antenna extension cables that will allow you to run it wherever you want.