From the book 'Wide-Body' about the making of the Jumbo it is mentioned that when a young lad one of the main desgners observed an engine fire in a B17or B29 that lead to the fire burning through the wing with the wing falling off killing all onboard, including the likes of the then Boeing Chief Engineer.
Said designer whose name escapes me never wanted to see that happen again so when Boeing produced the B47 which was one of their first large jets they thought about putting the engines in pods. This was to try to prevent engine fires resulting in wing structural failure.
Furthermore, as mentioned above, the effect of flutter can be reduced by using mass balances on the wings. According to the book Boeing engineers realised that these two factors could add to the safety of an aircraft which hence helped the adoption of engines in pylons for a number of reasons but particularly these two.