Arduino Mega & LIN Transceiver (MCP2004)
Should RxD be pulled up to 5 volt or 12 volt?


To 5V, or else you're out of spec with with the Arduino.


  Are the values for R1 and R2 ok?


Looks alright. RXD is an open drain pin. It will connect the resistor from floating +5V to GND when active.  


  I don't understand what to do with the V_REN pin?


My guess (from reading the datasheet) is that this circuit when used in an automotive application, is able to keep a connected MCU in reset/shutdown until the system voltage has stabilized. In the datasheet the circuit does this by using the V_REN pin connected to a voltage regulator that drives the connected MCU. The voltage regulator is implied to have a shutdown pin or similar that can be controlled by V_REN. The reason to do this is that the LIN bus should not be disturbed by stray data when the vehicle turns on and the MCU might be in a undefined state.