To the OP - you said that you connected the HDMI from the Blu-Ray player 'directly to the amp.' You never said which amp you had but since HMDI only carries a digital signal, then the output from the Blu-Ray player is getting decoded by another DAC, in your amp. Do you have a home cinema amp?
The difference between CD players is mainly the difference in the DAC - everything upstream of the DAC just does the job of getting the 1's and 0's off of the disc and feeding it to the DAC (the one that every CD player has, built-in). And any CD player can get 1's and 0's off of a disc - if you could not do that 100% reliably, then CDs would not work for computer software, since every single bit must be perfect to, say, install an application from a CD. Bad transports can feed timing errors to DACs, so the transport does matter (unless you have a reclocking DAC), but it's mainly the DAC.
So if you are comparing the analogue output of your Blu-ray player to the same player's digital output fed to the rDAC, I can pretty much promise that the latter will be better, since as others have replied, how much can they possibly have spent on the built-in DAC?
But that's NOT what you are doing. If you are feeding your amp with an HDMI cable, then you are not listening to the Blu-Ray player's DAC - you are listening to the DAC built-in to the amp. And if the amp is an A/V receiver, then it might be putting the digital signal through some kind of DSP designed to home theatre applications. Furthermore, if this is the case, then you may have the whole system (and your ears) adapted to that sound, such that the raw analogue signal coming from the DAC to the same amp's analogue inputs does not sound right.
Plus maybe you've got a really sweet amp with a great DAC that's better than the rDAC. I have a friend with a Yamaha home theatre receiver and we determined that the amp's built-in DAC (once we turned of all of the digital DSP crap it was doing) clearly outperformed the AudioEngine D1 standalone DAC (which is nowhere near as good as the rDAC, but still).