Like many other breeds of dogs, your Doberman needs a place to call his own. This is a natural instinct left over from a time when dogs lived in the wild and needed a den to call their home. He needs one place in your home where he feels it is safe for him to retreat to when things in the house get to be too much for him.
You should never use your pup's kennel as a form of punishment, this will discourage your pup from wanting to be in it. You want the entire experience and going into the kennel to be a positive one for your pooch. This will make it much easier for him to see the kennel as his "den", a place where he can go and no one will bother him.
In essence, you are taking what is a natural instinct that has faded to a background need and bringing it back to the forefront of your pup's mind. By doing this and working with your puppy, he will learn to see the kennel as his private place or den. Working with your Dobie while he is a puppy will make this training go faster, as in the wild the puppies are kept in a small den while the rest of the pack is off hunting.
Be aware that Dobies grow very quickly. Start out with a smaller kennel at first and then upgrade to a bigger one as your pup grows. Alternatively, you can start out with the bigger kennel, just block it off to make it smaller at first. Your dog only needs enough space to stand up, turn around, and stretch out comfortably. More than that and he may choose a spare corner for a potty spot.
Beyond choosing the right size crate, you need to turn it from a metal and plastic cage into a nice cozy den for your puppy or he will never want to spend any time in it. The best way to accomplish this is to cover the floor with a nice piece of thick carpet. Buy him a comfy new bed to go in his den, add a few new toys, and a hanging water bottle. You may even want to use a blanket to cover the top, back, and sides to make it even more cave-like.
Beyond this, you need a large bag of your pup's favorite treats, tons of time, and a plethora of patience. It is going to take you a few weeks working with your pup until he masters the skill of staying in his den when you need him to, but in time he will see it this way and start spending time on his own in there.