A definite yes - the house is empty (by the instructions of Otto Frank in honor of Anne - the emptiness represents his families absence/his loss) - so nothing scary about that.
There are a few parts of the exhibit that show the holocaust but it is easy to protect your kids from those sights. They have a very nice bookstore that carries books for very small children about Anne.
Explain the story to you kid beforehand - it will help create a memory. Buy tickets on-line before you visit - lines can be long.
I took my children when the youngest was 5 and they remember it well and in a good way.
The story of Anne is still extremely popular amongst kids of all ages - and so it should be. It is not only a memorial but also a message of hope - and the strength of Anne's spirit.
As a side note - visit the children's wing at the Tropen Museum (tropical museum) - the kids tour is incredible!