The issue is that bin/cue files often have a combination of music tracks and a data track with their stuff.
I think that if you do the conversion you won't get the audio tracks into the ISO file. However if it's just like a video movie or whatever, then that is data only and you shouldn't have a problem.
You can probably just open VLC up.
Through the file menu, goto "Open Disc"
and then you'll have something like dvd:///dev/hde
Select what type of 'disc' it is, like a video cdrom or dvd disk..
then change it (say it's a dvd) to:
dvd:///home/username/videodisk.iso
and that should be it. I haven't tried VLC with that, so I don't know if it will work, but I've done it before with mplayer.
The bin/cue thing is a propriatory format just for nero.... If there are combination audio/data tracks then you'll loose the audio tracks with the conversion, I beleive. There is Nero for Linux, but your best bet is probably just to burn the thing to disk from Windows and then rip the data from the disk in Linux or Windows using whatever sort of program you prefer.