It's really not a problem. Because my Ted E. was so terrified when he was little, I let him come out to me. I never put my hand in and took him out of his cage. I still do this for him. If I open the door and he doesn't want to come out, it's fine by me. If your little one prefers the tube, go with it. I look at it as respecting their space. Whatever works
Edit: With my dwarf hammies...they were territorial and would bite if I put my hand in their cage. I used heavy suede gardening gloves to get them out. It worked too. I wasn't so worried that I'd get bit and they learned biting didn't do anything for them. I can pick Almond up now without gloves.