Some airlines are picky about gps units, which is just plain stupid. But for those that do allow it, personally I found that I could generally get a reasonable signal for most of the flight in the window seat. I've been able to get it to work well in a window seat by putting the tray table down, using the auto beanbag mount, and then kinda angling the antenna towards the window. That was with my older Garmin 60CS. With my newer 60CSX I'd expect to work a little better, because it's noticeably more sensitive.
I like to know what I'm looking at out the windows, so I like to use it if I get a chance.