I would most attribute it to the audience for both shows.
Back in 99 the majority of your audience was the casual fan in their 20s or 30s who were there to drink and get rowdy. Today your fans are a mix of families and hardcore fans. While they may be more passionate toward the product, I don't think they are going to be as vocal.
I would also take into account the product that was shown then vs now. Not to say one was better than the other, but back then you had the more adult themed over the top stuff which lends itself to a rowdier crowd. Kinda like how the trashy morning talk shows of that time had lively crowds because they were getting feed over the top material that brought out that kind of response.
I agree that the product of 99 vs. today is a large factor. Sure, it's easy to say that the crowd of one era is different than the crowd of another. But, in the case of the Attitude Era, that was a completely different product.
I can only speak back to the Golden Era, starting (for me) in 1985-86. Those crowds would get vocal, but exactly how the characters and scripts wanted them to get vocal; cheering good guys and booing bad guys. I was 10 years old when I was in attendance for SummerSlam '89 and I remember thinking how loud it was when Warrior pinned Rude for the IC belt. I had been to house shows before, but not a PPV; so, I just thought that's how PPV crowds sounded. Years later, I would read how that specific pop was known for being one of the largest of that era. So, it seems it WAS as loud as I thought it was.
Next was the New Generation Era and I had not only stopped attending events by then, but stopped watching as often as I had during the Golden Era (which I would never miss!). But, the New Generation Era was full of Golden Era superstars and a new crop of superstars. So, the reactions seemed to be similar, as far as cheering good and booing bad, but quieter--probably because it was an era of aging veterans and unknown youngsters, leading to less-than-thrilling angles and matchups.
Then we got to the Attitude Era. Now, those unknown youngsters were major players and changing the game. Cheering good and booing bad was not a foregone conclusion anymore. Stone Cold and others changed all of that. Plus, as mentioned above, the wrestling took a back seat to more risqué angles. This is when it really went from wrestling to wrestling-themed drama.
Once the Attitude Era fully morphed into the PG era and whatever today's era is called, the product returned more to wrestling (and WAY too much talking), but less risqué segments. However, the crowd was now made up of all of these different fans from different eras. Those who are there with kids, ready to cheer good and boo bad. Those who are open to cheer for whoever entertains them the most, regardless of face or heel. ...and then the other group of fans. The ones who, in my opinion, take away from the show. The "smart" fans, or so they are called.
Granted, the lines between good and evil, as far as characters go, are far more muddied than they were in previous eras. But, there are still faces and heels. These fans, far too often, boo the faces and cheer the heels for the sake of booing faces and cheering heels. Their reactions seem as pre-determined as the matches they're yelling through. Roman Reigns is a good example. People loved Reigns in the SHIELD and were going crazy for him at the 2014 Rumble. Then, they were TOLD to like Reigns and instantly hated the guy. The same guy, mainly because he was "shoved down their throats". Maybe he was a bit...but these are the fans who shall not be told what to do! They are there to rock the boat because they think what they say steers the ship. The unsilent minority. They're going to events solely to takeover shows and then run home to see what the internet thought about them. When I read that SummerSlam '89 was a hot crowd, my mind did not go anywhere near "I was part of that". But these guys KNOW (in their minds) they were the voice being heard on TV.
It used to be people went to a show to be entertained by the performers. Now, a lot of people go to the show to be part of the show...and they're not. Not in a good way anyway.