gksudo nautilus NOT

After much frustration dealing with copying/moving/renaming etc files/folders, Someone told me about gksudo nautilus. Used it a few times and pretty much uh, love it. Then, I got the following advice from someone much more knowledgable than I:

"As a suggestion please don't use too much Nautilus as root user (i never use it as root) or will find some permissions issue when you are using applications software as unprivileged user...Please prefer to change owner (and or permissions) of files you want manage.."

Huh? So back to terminal??? Could someone explain this? Pretty new with Linux (8.10-64) and it took me hours to copy a file from my desktop to a folder somewhere down deep in the tree, .. and I still could not get it done with terminal. Took me about 10 seconds with gksudo nautilus (terminal) and Nautilus. I am not sure what the advice is actually saying ... because without using gksudo, Nautilus seems almost worthless, so I must be missing the point. Thank you.