Yes, a bubble just means that it's over-valued and that at some point there will be a significant correction in stock values. It doesn't mean that the thing is inherently worthless.
But also, a lot of the dot com companies that people invested in in 1999 went bust, meaning those specific investments went to zero even if the web as a whole was a huge success financially.
I started working in 1997 and lived through the dot com bubble and collapse. My advice to people is to diversify away from your company stock. I knew a lot of people at Cisco that had stock options at $80 and it dropped to under $20.
Because of the way the AMT (Alternative Minimum Tax) worked at the time they bought the stock, did not sell, but owed taxes on the gain on the day of purchase. They had tax bills of over $1 million but even if they sold it all they couldn't pay the bill. This dragged on for years.