Quite simple. Nature abhors a vacumn, and a decline in one species will generally be offset by proliferation of another.
According to the article the usual large predators such as cod have been reduced in numbers, meaning that now man can directly consume the now abundant herring, shrimp, crab and lobster that would have been eaten by the cod. How is this bad? How many pounds of lobster does it take to grow a pound of cod? Personally I enjoy lobster more than cod, and it is more efficient for me to eat the lobster than to let cod feed on it, and then eat the cod.
Likewise with your analogy with elk and buffalo, the ecological niche once dominated by them has now been filled with deer, cows, and people. Personally I enjoy eating venison and beef more than elk and buffalo. I also enjoy the company of my friends more than that of elk and buffalo. Is this bad?
No one is claiming that elk, buffalo, or cod are in danger of extinction. There has just been a shift in the proportional space these species occupy in the environment. I know of no "Divine Law" that holds that the numbers of these species must be maintained at the level they were in 1890AD, 1490AD, or 15,000 BC for that matter.
I see nothing inherently bad in a changing enviroment. Environmental change has been occurring since life began. I also believe that most humans are able to adapt to change, and can learn to get by on shrimp and lobster, or venison and steak when cod and buffalo are not plentiful.