I made a circuit in Logisim that reflects the D Flip Flop on this page:
http://www.play-hookey.com/digital/sequential/d_nand_flip-flop.html

The circuit works as the play-hookey diagram.
When CLK goes from 1 to 0, whatever is in D goes to Q.

But if I start a new circuit and use the first D Flip Flop,
the ouput lines are red.

Question 1.
Why are the lines red?

Question 2. Is there an easy way to reset Simulation?
I've been doing this:
D1
CLK1
D0
CLK0
When I do Ctl R, some lines go red.

 

Using an Inverter on one of your "Q" output will create a "0" when you reset. Also, a NO switch for your clock input will assure that the clock will not activate to a "1" when reset.

 

The lines output are red because the D Flip Flop is being clocked after reset.