The answer has always been in the source of flamegraph.pl:

  # This was inspired by Neelakanth Nadgir's excellent function_call_graph.rb
  # program, which visualized function entry and return trace events.  As Neel
  # wrote: "The output displayed is inspired by Roch's CallStackAnalyzer which
  # was in turn inspired by the work on vftrace by Jan Boerhout". 

Neel's did upward "flames" and I think CallStackAnalyzer did as well from memory, so based on the ones I was familiar with this was the precedent. We were also dealing with stacks that were commonly less than 30 frames deep, so it tended to fit on the screen. Also in my original flamegraph.pl implementation was an option to invert the flame graph (--inverted), so I've always let people choose. But I guess I had to pick something as the default.

Neel's was the biggest direct inspiration. I changed it to put the alphabet on the x-axis and reduced the color hues, but they look similar.