There are many differences. This is in the "beating a dead horse" category of argument because the difference between driving up to an intersection and biking up to one is so intuitively different if you've done both of them. But here are some reasons off the top of my head of why it is safer to yield through a stop sign on a bike vs a car:
1) On a bike you are much more towards the middle of the intersection so there is more space between you and people potentially entering the intersection from the sides, so you have more reaction time to deal with them
2) Your cross section is really tiny and entirely in front of you so there is no risk of hitting something you don't see
3) You have a much better field of view because you aren't obstructed by your car interior
4) You can use your sense of hearing to listen for cars/ pedestrians / other dangers
5) You are going much more slowly