I happen to work for one of those 50 companies, which gives me a little bit of perspective (even if I am very far down its hierarchy). And I can tell you that most of those companies aren't in that position because of a conspiracy of control - but because you have a pension. AXA, Legal and General, Aviva, Sun Life, and many many more of the companies on there are there because ordinary people put their cash into life insurance or pensions, and that cash is then invested in the stock market so that it can make payouts in the event of either problems (for the insurance) or retirement (for the pensions). And because many of these companies provide pensions either for millions of people, thousands of large companies, or both, they are managing massive piles of cash.
Which doesn't mean that they're actually running the companies they own lots of shares in. Most pensions/insurance/life companies are terrified of telling the companies they own shares in how to behave - they want to own shares in something successful so that they make profits, but they don't have the time to micro-manage them, and they really don't want to get involved in anything that smells even slightly political.
This actually leads, sometimes, to insufficient control over the directors of large corporations - because if you're in the FTSE 100, you're going to find your shares are owned by a lot of investment companies, who just want you to churn out profits, without paying too much attention to, say, board-level renumeration. So you can get away with paying your high level people a lot without a share-holder rebellion. If they were owned by a few ordinary people then they'd find themselves subjected to a lot more scrutiny, and a lot more control.
The reason there are central nodes that link together huge numbers of companies is because when you bought life insurance* you went for a name you knew, and so did everyone else. If you want to prevent that the answer is to use (or form) local, mutual, societies instead.
*Or an ISA. Or started a pension. Or opened a bank account. Or took out a mortgage.
Original post on Dreamwidth - there are comments there.