Most airlines have a policy that when taking off or landing (practically speaking while the seatbelt sign is on) ALL electronic equipment should be turned off. Not getting into a debate here about whether or not that is necessary; those are the rules; simple.
At other times, ie in the cruise, you can shoot what you like out the window, no issue at all.
An issue does arise if you start taking the cabin interior, as someone else said this is a privacy issue. On board an aircraft, like anywhere else, you should not photograph someone (esp the cabin crew) without asking their permission first!