Why no sequel

Despite being a box office what exactly?

It simply didn't go over well with critics or audiences. You can't judge the quality of a movie by box office receipts because often audiences will flock to a movie for a number of reasons (the stars that are in it, hype, previews) only to find it's not a good movie and by the time word of mouth gets around it's already raked in a substantial amount of money. The Flintstones had a lot of stars as well as the curiosity as to how a live action version of a popular cartoon series would turn out. Like most attempts at making a movie based on a TV series, it just didn't turn out well. It had its moments for sure, just not great and I don't think it was popular enough that audiences were clamoring for a follow-up.

I agreed that the prequel follow-up was dreadful.

I wish it had a sequel right now! ?

This video does into detail about the film's production:
https://youtu.be/H_MCQwiGUHg?t=1076

Apparently, John Goodman didn't really care much about the project and he really only did it as a favor to Steven Spielberg. Goodman was worried about being typecast as Fred Flintstone for the remainder of his career and humbly requested to be released from his contract, which called for at least two sequels for Amblin.