What you are seeing is that, even though Virgin is huge and expensive and provides a lot of value, the industry is competitive and very little of that value is profit to the owner. Whereas Minecraft has a niche and is very profitable.
"Here a durable competitive advantage has proven elusive ever since the days of the Wright Brothers. Indeed, if a farsighted capitalist had been present at Kitty Hawk, he would have done his successors a huge favor by shooting Orville down." – Warren Buffet, who invested in US Airways in the early '90s, on airlines in 2008
It's a really profitable industry these days. Low oil prices reduce costs. Plus, ticket prices haven't gone down because routes are consolidated to reduce competition between airlines.
Haha! Well if you compare that way, there are numerous examples of a piece of software doing well(or have more market cap) than a physical company with many machines and thousands of employees!
There was a Tumblr that had a list of things that are cheaper than Whatsapp's $16B acquisition. It's pretty insane how much bigger of an industry some things are over others.