Some reasons it was seen as more physical:
More post play. Few guys today back down in the post anymore. In the 90s, MJ, Barkley, Admiral, Ewing, and other superstars made their living off backing down from about 15 feet away. I notice that people perceive that as more physical, probably due to the body-to-body contact that has become less common these days. And fewer of these players flopped offensively to draw fouls while playing in the post, which viewers (self included, I admit) see as soft.
More hand checking. The rule changed in 2004, when defense on the perimeter got a bit softer. There were actually more fouls called back then, funny enough -- 22.7 fouls per team/per game in the 90s vs 19.6 now.
https://www.statmuse.com/nba/ask/nba-league-average-personal-fouls-per-game-by-decade -- But having the hand check rules allowed guards like Muggsy, Mookie, MJ, Glove, and Stockton to play much more physically on the perimeter, even if they also got penalized more than guards do nowadays.
Rodman being Rodman. He made every game he played in, many of which were transmitted across the world, feel like a wrestling match.
Knicks vs. Pacers, Knicks vs Bulls. Dale Davis, Charles Oakley, Horace Grant, Scottie Pippen all went at it. These were big series played on a major network.
The premiere of Shaq dragging his boys across every center's face, also getting fouled hard without the refs knowing how to call the game. That led to defensive rules changing, allowing more zone defense to be played in the NBA, which reduced defensive contact.
Zo, especially on the Heat. Mutombo, on the Nuggs and Hawks. Games they played in felt more physical because they were all physical specimens who imposed their will. You could say the same about the Admiral.
All those things. But also, it was a game with less spacing than today's game. Players were closer together, contact happened more often without whistles. Flagrant fouls weren't punished as severely as they were in later years, especially post-Malice, meaning there was more incentive to foul the hell out of players driving to the hoop. That likely lead to more violent fouls at the rim, but also likely incentivized players to take more mid-range jumpers.
TL DR: The 90s game wasn't necessarily more physical -- guys today are superb athletes and any star today would do just fine in the 90s -- but it was a game with more contact allowed, more post play, less spacing, and more big-man dominance.