Not all puppies do well with crate training as a method of housebreaking. Some puppies take to it easily, but others don't like it for a variety of reasons and will cry and not settle down. With dogs like that, you may need to find another method of housebreaking.
Dogs are pack animals. They are used to being with other dogs. Highly social, dogs don't do well when they are left by themselves. Indeed, in the wild when a wolf pack leaves a wolf to his own devices, it's not a good thing -- it means the wolf has been ostracized. If your puppy's crate is located away from where everyone else is, the puppy will whine and cry. Many times, this makes it worse because the owner, seeking peace and quiet, will move the crate to an even more remote location. The puppy's crate should be in the living room when the rest of the family is in the living room, and in a bedroom where at least one family member is sleeping so the puppy is not lonely.
Leaving a puppy in the crate too long will not only defeat the purpose of using the crate for potty training, but is inhumane. Young puppies cannot "hold it" for hours on end. The longest a puppy should be left in the crate is four hours at a time during the day, and eight hours at night. If the puppy is crying when left too long in the crate, he may be trying to tell you he needs to go out. If you are not there to let him out, or you ignore his cries, he may soil in the crate. If this happens too often it becomes habitual. Once that happens, you have a bigger problem on your hands. Not only are you teaching him potty manners, but you are trying to break a habit as well.
Some people use the crate as punishment. If the puppy is caught chewing something inappropriate, or if the puppy has an accident in the house, you may be tempted to put him in the crate for a little time out to teach him a lesson. This is a bad idea. The whole idea behind the crate is that it supposedly simulates a wolf den. Dogs like the idea of having their own little nest, or den, to which they can retreat when stressed, tired or scared. If, while using the crate for potty training, you leave him in there too long out of anger, or because you are punishing him, he will learn to associate the crate with negativity and your efforts will be thwarted.
Some dogs don't like being confined in the crate. Rather than seeing it as their "safe place" and using it like a den, they see it as a prison, a barrier to being with the rest of his pack (you and your family) and they learn to hate the crate. This is a real risk if the puppy is left too long in the crate because he never knows when he will be getting out, so he cries and cries out of boredom, fear or anxiety. Separation anxiety is a very real problem for many dogs and should never be dismissed as just a phase or a character flaw in your puppy. If you see signs of separation anxiety (soiling the crate, biting at the bars, crying or barking incessantly) it may be that using crate training as a method of housebreaking is not the best choice for your dog.