1. Bus seats tend to be extraordinarily narrow. The sitting in generally much more comfortable on a train.

2. The RER will deposit you at one of two or three city stations, where you can then transfer to the subway to your hotel. This just seems more convenient than taking the bus, then locating the subway, then entering the subway (hassle) and finally taking the subway to the final destination.

Let me say I've never taken the bus. It might be a much better deal than I imagine. Since the OP needs to get downtown somehow, perhaps you could describe the bus ride in some more detail. Who knows, I might take it one day!