I believe because JFK's dad was obviously in the bootlegging business,as was LCN.

Once Chicago and NY got their grips into the Prohibition money, they told JFK's dad what HE MUST pay them....He probably was not up to date on what he owed them BUT, claimed that once his son became president, THEY would be paid back in a way that only a President can do. I would guess that THEY wanted pardons for jailed members. Maybe even a re-entry for Lucky.

JFK could NEVER grant a pardon as such in the beginning of his term. Impeachment city!

JFK couldn't deliver on the promise his dad made to LCN....So, they chose to make Sr. feel the most pain. Burying his child.

My theory!