I plan to add a setting for that in the future. It will allow you to select where you want to display the messages sent via d()/AddMessage() and also the ones sent via LibChatMessage. It was just a bit beyond the scope of this first release, since it will require additional code and I just wanted to get it out the door.
If you really don't want it to hide the messages from chat, you can remove line 74 in StartUp.lua (
LDL:SetBlockChatOutputEnabled(true)). Then they will be shown in both chat and the quick log.