The first time Thor and Surfer fought, Surfer had already been drastically depowered from his encounter with the sonic shark...this was done to prep Surfer for his own series (he was considered too powerful to be a leading character--too hard to write stories for, since he was confined to Earth).
FF#72 - Surfer (referring to the sonic shark): "It has...almost totally drained me...of my cosmic power."
FF#74 - Surfer (speaking as he blasts Galactus' Punisher): "Though my own power is but a fraction of what it once had been...perhaps I can still muster a strong enough atom-compacting thrust!"
FF#76 - Surfer (while being attacked by the FF): "Though I no longer possess the limitless powers of the cosmos...still am I the Silver Surfer!"
FF#77 ... SS debuts for first time in his own mag--referred to in this FF issue.
SS fought Thor, what, 4th issue of that series? Based on the continuity from the FF mags, clearly, Surfer was not in top form. Even with Loki's power added, he was still not what he was (he fought Loki to a tie, implying the best Loki coulda done was simply double Surfer's current power level...still far less than his pre-sonic-shark days).
The second time SS and Thor fought, Thor had warrior madness--which increased his power Ten Fold! And still, SS was able to hold his own until the very end.
Thor does not have Surfer's durability nor his speed, and while he may have some power versatility, Thor generally punches and hammer-smashes. When he does use his most powerful blasts, it also takes a few seconds or so for Thor to "warm-up." Surfer would not give him those seconds.
Biased I am, but I suspect an ulterior motive on Marvel's part.