I don't think you have anything to worry about. I have always noticed the pulse in my stomach. Sometimes it's more noticeable than other times.
I will say one thing, not to scare you, and in your case, I am sure this is not the cause, but sometimes, aneurysms can cause this, but, they are normally in older folks with high blood pressure. Like I said, don't be afraid, and the only reason I am saying this is because I want to cover all bases as to why this problem can be observed, if it continues to worry you, ask your doc, but I bet he tells you the same thing, and if he does test you, it is very easy, it is just an ultra sound of your aorta.
I have heard of this before however, and my mother experienced it, no, it is usually not serious. I know the aorta extends into the tummy and that is a big vein, so, it would not be too unusual to see it, especially if you have been working out and your heart is pumping harder than normal. The same with the neck, lots of folks can see their veins beating. Do you have thin skin? I am glad your doctor said you were in good health, even if you did not ask him, if something were wrong, he would have picked it up during the physical.
I hope this helps, and again, don't let the part about the aneurysm scare you, there are lots of other symptoms usually associated with them and you have not indicated any of them. So, try to relax and maybe if you just ignore it, it will go away.
Susie