I am sure some or all of these ideas may have been brought up already, but just wanted to give my thoughts on this whole thing.
Trump spent the end of the election cycle claiming the election would be rigged, which caused his opponents to defend the system. We now know that his chief strategist, Steve Bannon, uses misdirection as his main weapon (see the recent interview with him). Maybe, just maybe, Trump's rants about the rigged election were done on purpose, to force the media and his opponents to defend the system. All the while, maybe there were some shenanigans going on. Now that there might be hints that some form of rigging did happen, everyone who defended the system previously will be ridiculed for questioning the very system they were forced to defend over and over. You can already see this at work in this thread and any other thread about this news article.
The other thing that I really wonder about was Trump's claim that if he lost the election it would be a huge waste of money, 100 million dollars by his estimate. At the time, every news outlet that looked into his claim that he spent that amount of money on the campaign could only find evidence that he spent between 50-60 million dollars of his own money. Most seemed to dismiss the figure he was throwing around was just another Trump embellishment, which hey, it very well could be. But on the flip side, maybe that figure was accurate, and maybe he did funnel some of his money into places and people that the public was never meant to see or know about.
From the investigative reporting done about Trump during the election, we know he is perfectly comfortable breaking federal laws to try and further his own interests. See Newsweeks reporting done about his illegal attempt to do business in Cuba.
I am not sold on the idea that there was some fraud, rigging or hacking, but from my perspective there are enough questions being raised about the results in some key states to warrant an audit. Why not be certain of the results?