If you are talking about Superman Prime of the DC One Million reality, he is able to take Rune Thor along with all the other terran gods and crush them with no effort at all.
After Superman left Earth, his travels lasted from the 21st Century, and ended somewhere at the turn of the 700th Century. During that time, he acquired vast abilities and skills from every being he meet and gained perfection over all the abilities he received (when he broke through the Source Wall he even studied under the
Source itself, meaning he could have a portion of the Source's power or more, the true extent of abilities he received from the Source are unknown).
He also has gained the abilities of his lineage and magnified them with his own power (for example, the Superman of the 67th century married the queen of the
5th Dimension, GZNTPLZK, which in turn gave Superman Prime the abilities and powers of a 5th Dimension Imp).
The time he spent in the sun magnified his already immense power to seemingly infinite levels; he could weave all of time, space, and shape reality at any level he desired. His strength and other countless abilities he gained also rose to infinite levels from the time he spent in the sun; he can seemingly destroy and recreate everything from a planet to even a Universe or an entire reality.
In short, Superman Prime has acquired countless powers and abilities from his travels and lineage that allow him to do almost anything he wishes, his power range from teleportation to the manipulation of magic and reality. He can manipulate time, space, matter, and bend reality on any scale he wishes.
How can a god born of the biosphere of a second rated planet match that?.
And don't come again with the crazy idea that Thor has greater "battle experience". Nordic goods battle skills are a reflection of the way vikings fought and they were by no mean good fighters, proof of that is that they only ravaged defenseless villages and towns and quite rarely found real armies. Thor way of fighting lacks the finesse of a real swordman, a master archer or a martial artist. Besides that this is not a physical battle, however Superman Prime strength is now limitless.
PD: oh yes, I forgot to add the fact that Superman Prime holds the legendary last ring of Green Lantern, one of the most awesome weapons ever created and more than able to render mjolnir useless.
