Part of this is the difference between "muddiness" and "clearness" of tone. Part of it is the projection and dispersion of bass notes. Adding some high-mid and higher freqs will make the notes more distinct and easier to pick out. Play at different octaves to see if it still sounds like the right note. Play the typical companion notes (5th, etc) and see if they still sound right as well. Don't have your amp pointed at your ankles. Don't play louder than you have to.
If you're listening to recorded bass, much of the more "modern" stuff (and pre-60's stuff as well) has very messy production and can be hard to distinguish. As well, many times there are multiple bass tracks, sometimes with different tones or presence, sometimes with different notes, all combined into one "bass track", and that can make it hard to really tell what's going on.
Add to that odd or sloppy tunings, sloppy tuning centers, and sloppy performances, it can be hard to hear it sometimes.
Some people are more disposed to hear bass than others, and that is often the case with people who have chosen to pick up instruments in that register.