Hearing a dog whine from inside a crate can be heartbreaking -- which is why Rover's doing it. He's counting on you feeling bad for him and letting him out. Of course, the more you cave in, the more he'll whine the next time you put him inside the crate. Even if the sound is driving you crazy, figuring out a routine and a way to get Rover to stay in the crate is important if you want the crating to be a success.
Get him used to the crate a bit at a time, rather than just putting him there for hours. For example, the South Florida Siberian Husky Rescue recommends creating positive associations with the crate -- such as placing a treat or a toy into the crate and allowing Rover to walk in to get it. Don't close the door at first -- just let him walk in and out so he feels comfortable with the space. Then start closing the door as he walks in to get the treat, wait for a few minutes and then let him out. Keep increasing the time that the door remains closed. This will allow him to feel comfortable -- and to know that the door eventually opens and everything's OK.
Make the crate a comfortable place. Aside from adding a toy and a treat, put Rover's favorite blanket inside. Dogs might whine while in the crate because they are bored and just want to get out and be part of the activities going on in the house. If that's the case, give Rover a fun interactive toy, a bone or a chew stick. Let him entertain himself -- he'll soon discover that it's not really that bad there.
Add a T-shirt or something else with your scent to the crate. This will especially help if the crate is in a different room, where Rover can't see you. This might not immediately calm the whining, but it will eventually help Doggie realize that you're still around -- or at least your scent is.
Ignore the whining. Some dogs will cry, whine, howl or bark while in the crate. The minute you respond -- either by yelling or by opening the door -- they'll learn that that's their way out. If you can't help yourself, move the crate to another, quieter room and close the door. Saying "no" in a firm voice -- without yelling -- can also help. Simply say it once and then go back to ignoring him.