The article is very long (I suggest you read it anyway) and it mostly focuses on the Wilpons association with Bernie Madoff.
There's some interesting backstory in there: the Wilpons and Madoffs first got together when Jeff Wilpon met Mark Madoff at Roslyn High School.
The story doesn't really shed new light on whether Wilpon knew that Madoff was a fraud. But it does raise a pretty good refutation: if Wilpon did know the nature of the scam (a Ponzi scheme) why did he keep $550m of paper money in his Madoff accounts?
I think it's more likely the Wilpons suspected he was doing something illegal or questionable (insider trading maybe) and chose to look the other way. I doubt they would have thought a Ponzi Scheme of this magntitude could have lasted this long.

Barring all that, here's the part of the article that has everyone talking:
"In the game against the Astros, Jose Reyes, leading off for the Mets, singled sharply up the middle, then stole second. “He’s a racehorse,” Wilpon said. When Reyes started with the Mets, in 2003, just before his twentieth birthday, he was pegged as a future star. Injuries have limited him to a more pedestrian career, though he’s off to a good start this season. “He thinks he’s going to get Carl Crawford money,” Wilpon said, referring to the Red Sox’ signing of the former Tampa Bay player to a seven-year, $142-million contract. “He’s had everything wrong with him,” Wilpon said of Reyes. “He won’t get it.”
After the catcher, Josh Thole, struck out, David Wright came to the plate. Wright, the team’s marquee attraction, has started the season dreadfully at the plate. “He’s pressing,” Wilpon said. “A really good kid. A very good player. Not a superstar.”
Wright walked.
When Carlos Beltran came up, I mentioned his prodigious post-season with the Astros in 2004, when he hit eight home runs, just before he went to the Mets as a free agent. Wilpon laughed, not happily. “We had some schmuck in New York who paid him based on that one series,” he said, referring to himself. In the course of playing out his seven-year, $119-million contract with the Mets, Beltran, too, has been hobbled by injuries. “He’s sixty-five to seventy per cent of what he was.” Beltran singled, loading the bases with one out.
Ike Davis, the sophomore first baseman and the one pleasant surprise for the Mets so far this season, was up next. “Good hitter,” Wilpon said. “Shitty team—good hitter.” Davis struck out. Angel Pagan flied out to right, ending the Mets’ threat. “Lousy clubs—that’s what happens.” Wilpon sighed. The Astros put three runs on the board in the top of the second.
“We’re snakebitten, baby,” Wilpon said."
Let's take all the claims separately:
Jose Reyes is not going to get Carl Crawford money because he's always hurt. Indubitably that is accurate.
David Wright is a very good player, but not a superstar. I could publish reams of statistics supporting that claim but I don't think I need to.
Wilpon was a "schmuck" for giving Carlos Beltran $119m. I disagree with this one, but its a popular opinion. He had a very bad 2005, a great 2006 (marred by one negative image), very good 2007 and 2008, then two years ruined by injuries.
Ike Davis is a good player on a "shitty team." Wilpon said that when the team was 5-13. Even now at 22-24 I'd agree with the assessment.
I just don't see how anyone can take issue with anything he said as far as its veracity, whether an owner should be that honest is another matter, but I personally enjoyed his candor.
As for him hurting the trade value of Beltran and Reyes, can you imagine any GM in the majors who changed his opinion on either of these players based on Wilpon's comments? That's a false argument.
There's a lot of hate for Fred Wilpon (much of it comes from anti-Semitism I believe) and very little of it has any basis in fact. He's not cheap, he's spending $144m for this last place team. He's not the problem with this franchise, payroll is in the top 10, results are in the bottom 10, that's the fault of the players and front office (his blame for that ends and hiring those fools). And he's not ripping his players, he's just being honest.