What does, "It can't be regenerated" mean?
Well, no. Regenerate has a very specific meaning. From the Comprehensive rules:


  701.12a If the effect of a resolving spell or ability regenerates a permanent, it creates a replacement effect that protects the permanent the next time it would be destroyed this turn. In this case, “Regenerate [permanent]” means “The next time [permanent] would be destroyed this turn, instead remove all damage marked on it and tap it. If it’s an attacking or blocking creature, remove it from combat.”


So, what Golgari Thug did, was not regeneration. Instead, it put a creature from the graveyard on top of its owner's library. Regeneration would have stopped the creature from being destroyed and placed in the graveyard in the first place.

Putrefy specifically prevents creatures from being regenerated after being destroyed by its effect. This doesn't counter regeneration (at least not in the MtG sense of the word), but prevents regeneration from happening. 


  101.2. When a rule or effect allows or directs something to happen, and another effect states that it can't happen, the "can't" effect takes precedence.