Tubes are very much like burrows - and thus considered "safe" by little hamster brains.
That's why I provide my Robo, Dave with so many - as a very timid little hamster, she's got plenty of opportunity to duck out of what she doesn't like.
Harry, our rescue, currently sleeps in his tube - it's where he can't be got at.
As they become more comfortable, they'll move out of that - it's just a matter of time