From what I can gather it is derived from the automotive industry standard CAN (Controller Area Network) bus, but I was wondering if they share the same protocols. If you took an automotive bus reader and hooked it up to a ARINC 825 system would it read the same?
Yes, the underlying CAN protocol is the same. The 825 standard specifies some CAN IDs/priority scheme for standard purposes, similar to the ARINC429 label standard. It also specifies certain CAN bit timing configuration, such as 1 sample per bit at 75% of the bit time, and re-synchronization jump width at 1 time quanta. These are all settings in the CAN standard.
This datasheet provides some hints, but unfortunately being an ARINC standard there isn't much public information about the label and data structures.
If you connect a CANBus tool that supports extended ID's you should be able to see the CAN data. The bus is comparable at a CANbus and electrical level.