Because it was Putin as an individual who made the key moves to remove democracy and install himself as the autocrat. Putin was not just a cog in the system. He was the central force making these intentional decisions that caused this outcome. If Putin didn't want to make Russia an autocracy, and instead he as an individual preferred democracy, then that's what would have happened.
1990s Russia is quite dissimilar to other situations in history where there isn't one person causing the outcome. For example, regarding Japanese history of 1930s/1940s, it was not one kingmaker, it was a long chain of events and decisions involving many people. Your thinking would be correct if applied here.
It's true, however, that Putin's moves wouldn't have been possible without the situation that he found himself in ... a weakened Yeltsin, dire economy, and nationalist sentiment after the apartment bombings. Putin capitalized on these things to get power. But once he was in power, it was mostly him.