In the most recent chapter, something interesting was revealed. That former Government agent Jimbei was fighting was revealed to have been imprisoned for 12 years for allowing the Gomu Gomu no Mi to get stolen. Now, why is one little devil fruit so important that one would get arrested by the World Government for failing to protect it?
Well, the World Government has a habit of hating anything that undermines their power or makes them look bad. They killed an entire island because some of its residents were researching the Void Century, and when it was suspected that Roger may have had a kid, they had all the infants and expectant mothers of the last island he stayed at killed. So, if, let's say, somebody in the past had the Gomu Gomu no Mi and did something that was bad for the World Government, then it would make sense for them to want to keep that fruit under wraps.
Judging by the fact nobody in canon has pointed out Luffy's devil fruit in particular, it can be assumed that this Gomu Gomu no Mi user lived a lot time ago (long enough for their existence to be covered up and forgotten by all but a few). To me, it'd make the most sense if this user were someone important from the Void Century. Maybe it's Joy Boy, or maybe it's someone else that caused the World Government a lot of trouble.
Alternatively, maybe some World Noble just wanted that devil fruit and threw a hissy fit whenever they didn't get it, who knows.