Have you checked the volume of your source, in this case the laptop?
In my own experience (Probably I´m not right), when you connect a portable device such as Ipod, Cell phone, Laptop to your head unit, the voltage of your primary source is not equal as the car. I mean, probably the output of your laptop brings 5V, and the car is 12V. In almost all the aftermarket stereos, the RCA output brings 2V, but this signal will be connected to a power amplifier, and then you compensate this lost, although you probably need to level up the gain. If you connect the speakers outputs (not RCA, 12V) from and aftermarket stereo, you can notice that the gain level from an amplifier must be kept low, this is because the power of 12V is "sourcing the amplifier". In few words, in your stock sound system, you will require a powerfull amplifier to hear this Loud. Remember that the stock sound systems are designed to be heard "loud", but always there is a limit.