I realize I am a bit late to this post. As a father of a 3 year old and a 10 year old, I have no fear traveling to these places. My family visited Munich last year and stayed in a hotel outside the city center a few stops out and we felt safe, even when walking back to the hotel at night. In 2017, we are visiting Vienna and Salzburg.
Our first family trip was to Switzerland and Italy when our smallest was 10 months and oldest 8. Before we returned home, our oldest said she wanted to come back again! We went back last year to Bacharach, Munich and Fussen in German and Wengen, Switzerland.
My wife said she thought having children opened the locals up to us. In restaurants, we were normally the center of attention for the owner/waitstaff. Sure you have to reduce your pace and the expected amount of stuff to see every day, but it forced us to prioritize and to really go slowly. We planned something for the kids every other day. The first two years, we had nap time in the middle of the day, so we stayed close to the attractions we wanted to see and got an early start then came back for a siesta most days. The kids really enjoyed it. Our trips were 16 and 15 days each. We discovered that about every five days, we needed a down day to do laundry and rest and focus on the kids. Go to a park, or a beach.
As far as crime, I have no fear in violent crime. It is rare. I fear forgetting/dropping something important to the kids ( pacifier, tablet, favorite stuffed toy) more than pickpockets.
With luggage, make sure it fits together over cobblestone streets and stays secure. Before our first trip, I took the family on forced marches with luggage and made them carry their luggage up and down stairs to simulate train and underground stations. Our 8 year old and my wife, got rid of lots of useless stuff.
One thing to remember, trouble is trouble no matter where you are. A bad area in your town looks much like a bad area in a foreign city. If you feel you are in the wrong area, turn around or hail a taxi and get out of there. Pickpockets will blend in to the environment.
For our first trip, our seven year old was afraid of being seperated from us. So we went to REI and bought security whistles and put them on a string around our heads. She was told, that if she could not find us to stop and don't move. Blow the whistle for 10 seconds every minute. We went to her school and she and my wife went off and i had to find them. It relieved her main concern. We also took a picture every morning of the both of them. The 8 year old took a picture of us every morning as well. Before our trip, we started cooking food we would experience on the trip so it was not a shock to them and they were familiar with it.
If you have any more questions, feel free to message me.