It is. Your perspective is warped.
Having a six-figure household income at all puts you in the top 15% in the US. Having a $400k salary puts you very close to the top 1%. I would say anyone making enough to put them, by themselves, in the top 15% is arguably making a "big salary". The Valley has really warped the perception within this industry in particular and the US in general as to what "normal" money is.
400k is a good executive salary. i guess you could call it 'big' but it doesn't strike me as something 'too high' or as an indicator of something nefarious going on. it's in line with very senior executive pay at the c-level or a very senior VP/MD. someone like that probably oversees up to 8 or 9 figures of business.
Also, engineering societies generally are based in major cities.
I'm also not sure I agree that under $400k/yr is "big salaries". Especially in a company that can't offer stock, doesn't offer big bonuses, etc. I was offered a job there a couple of years ago, and spent some time talking to the CTO. She was remarkably candid with me about PLoS' financials and their plan for growth (which, I note, they've executed on marvellously). I have never, ever, ever been more impressed by an executive. If the rest of the executives are of the same calibre as Ms. Rayhill, they deserve every red cent.