Fruit is nice because it usually wouldn't have to be refrigerated right away. That can be quite a problem when many people tend to bring casserole dishes and such. Another reason that fruit is a good choice is that most people are able to eat at least some kinds of fruit no matter what their dietary restrictions might be. Also, like flowers, it adds a little color and life to a room - something pleasant to look at at a time when the world might seem grim.
In this area it's very common for the family of the deceased to mention a specific charity to give to "in lieu of flowers." I tend to lean toward doing that when it's their request. One of my DH's co-workers passed away a few weeks ago, and the request was for donations to the Wounded Warrior Project because the deceased was a proud veteran. The widow soon wrote a very touching thankyou note mentioning a young man they knew who was badly injured in war and who was helped by this charity.
Honestly, I think good people appreciate the thought that goes into cards, flowers or any gift you choose to give, and it's really best to do whatever feels right to you. If it's from the heart, you can't go wrong.