I've found that many organizations tend to have a 'dominant function', and CEOs tend to come from that function. So if engineering calls the shots in your company, or is the main driver of success, the CEO tends to come from engineering. If the company is driven by sales, the CEO tends to come from sales.
That's why you see so many oil company CEOs who are geologists or engineers, tech company CEOs who are developers, and CPG CEOs who are marketers.
Which explains why there are more Engineers in the 'top 50 Companies'; because most of the biggest, and most valuable companies, are Engineering based in some way, either by manufacturing a product (Cars, Planes, Computers), applying Engineering (Mining, Metal, Oil) or reliant on technology to perform their business (Telecoms, Internet).
The big exceptions would be Finance, Logistics, Business Consultancy or Conglomerates.
There are national trends too - the UK will draw from finance more than many countries, Germany from Engineering. If I had to guess I'd imagine that the US was more likely than many countries to have CEOs with a marketing or product background.
It doesn't dissuade from your point at all, but as a geologist in the oil industry, it's rare to see a geologist in upper management.
(One big exception: Tony Hayward, who's was also one of the few energy-industry CEOs to have a STEM PhD. (CEO of BP during the Macando/Deepwater Horizon blowout.) Other exceptions are mostly very small, exploration-only companies.)
The truth is, though, that the oil industry hires very few geologists in proportion to the number of engineers. (This is true even if you disregard the entire "downstream" refining and marketing half and just stick to exploration and production.)
The most common job function for most oil and gas companies is building or maintaining physical infrastructure of some sort. (e.g. wells, production facilites, pipelines, refineries, etc) Therefore, oil companies hire mostly engineers, and most oil company CEOs are engineers. (Once again proving your point.)
My sister's a petroleum geologist. She's said that there's a big supply/demand imbalance for geologists in the oil industry - universities will graduate only about 1/3 as many geologists as the industry needs over the next 10 years. Geology's one of the least popular of the STEM majors, and among geology college students, the oil & mining industries are often seen as "selling out to the man", since many geologists also tend to be environmentalists and the oil industry is...well, not.
She's perpetually overworked as well, which squares with a supply/demand imbalance. You'd think that this'd just lead to higher salaries - and by her accounts, her employer basically does throw money at her - but the fact that petroleum geologists are paid pretty well hasn't yet filtered down to university students choosing their majors.
There certainly is a big supply/demand imbalance, but undergrad geology enrollments are actually way up. All geoscience departments I know have have dramatically increased in size in the past 10 years or so. (e.g. where I went to undergrad has gone from 5 geo majors to ~60, and I've seen the same at the two places I went to grad school)
A lot of it is that a geoscience job at an oil company requires an M.S. or a Ph.D., and geology degrees typically take longer than most other fields. There's a minimum of a 6-year lag between starting undergrad and being eligible for a job. Typically it's more like 7-8 years total for an M.S. and 8-12 years for a Ph.D.
Therefore, it's a long pipeline. I just started in industry, and when I switched to geology in undergrad (early 00's), oil companies were not hiring geologists and hadn't been for 15 years.
The stigma associated with going into the oil industry depends a lot on where you are geographically. If you go to an "oil patch" school, then it's the opposite effect. It is a factor, but I'd argue the field vs. desk job part has a larger influence.
Geologists tend to become geologists because they _really_ like the outdoors. With a few exceptions, as a petroleum geologist, you're behind a desk 100% of the time. Compare that to fields like environmental consulting or state government work where you can start right out of undergrad and are in the field a significant portion of the time. (Both of those pay less and tend to involve less actual geology, though.)
Finally, there's a risk/reward trade-off. Geologists tend to be among the first to go when layoffs start. We're concentrated in exploration and development (note: field development, not software), and exploration is viewed as an expense, not a profit center. Exploration budgets get slashed the second things look like they're going to take a downturn, and smaller companies lay off most of their exploration geologists whenever oil prices drop. Development is the second thing to cut back on after exploration. A lot of the folks that I got my M.S. with started jobs in '06 or '07 and were laid off in '08 or '09. They've all since found jobs again, but the cycle will repeat itself.
That's why you see so many oil company CEOs who are geologists or engineers, tech company CEOs who are developers, and CPG CEOs who are marketers.