As the article points out, such a strategy means that newcomers to the market have to compete based on initial funding - not technology. And to claim that Google has a 'free ride' is rubbish - for that to happen it would have to be a one sided relationship, but here news being indexed by Google is mutually beneficial - with one partner starting to get a bit greedy.
Search is already fragmented with plenty of sites indexing private article databases not available to Google, how is one more going to make that much of a difference?
On your second point - search is by no means as fragmented as this would result in it being. The specialised databases you speak of are just that, currently our expectation is that Google, Bing, et al all index the web we see on a day to day basis. Ideally those databases (if they are already in some form 'public') should be indexable by all search engines - it's the best thing for the consumer, and is pure competition on the technical front.