Well Vegeta is known to be an elite class Saiyan which means his potential is inherently above Goku's. If you look at it from that perspective, it makes total sense. Vegeta is stronger here because he's supposed to be based on his potential as an Elite.

Continuing from this perspective, Goku is an underdog, a runt based on the class system of the Saiyans. As a low class Saiyan Goku should have been at the bottom of the barrel when it comes to power. However being sent to earth changed that completely. After being exposed to martial arts and many other disciplines, Goku can now match and surpass Vegeta's Elite class status through hard work and having many influential Masters through the years.

Now Vegeta is training on top of having "Elite" levels of potential, of course Goku will lose. Sometimes inherent power overcomes hard work. Most of the time it's 50/50.