Yes, you can take them off in customize, and be shoeless all the time.
However, you can't customize while in a private room, so make sure
you do it before entering the room, otherwise you have to leave and
come back.
You can put something in the suggestions forum about maybe being
able to remove the shoes while in the bedroom, such as clicking on
the feet or something, but as Cidney said, this is the only option as
of right now
DDC