1. The author worries about Apple crowning a successor. What they're advocating is HTML5, which is essentially an open standard, where Flash is of course proprietary.
2. The premise of the article is that Apple has the power to kill anything they set their mind to. It uses the lazy argument of the slippery slope or thin end of the wedge ("What's next?"). It's simply fearmongering;
3. It mistakes cause and effect. A classic example of this was Intel's original Centrino platform, which became the basis of Intel's success (after the Pentium 4 debacle) for years. At the time it launched Intel spent $150m+ on marketing it. Sadly, many observers attributed its success to that marketing campaign when in fact the lesson is:
Good products sell themselves.
Centrino succeeded because it was a good product.
Flash came about at a time to solve a problem of creating "rich" Internet applications ("RIAs") when it wasn't possible any other way. That's no longer the case with a plethroa of Javascript frameworks and browsers with fast Javascript engines in them.
The use case for Flash was going away anyway. Apple just hastened its inevitable demise. They haven't killed it. They just threw some oil on the fire that was already burning down the house.
4. Apple is on the outs with a bunch of other companies? Large companies are complex creatures. You will find them competing savagely on one level while cooperating on another. But the real reason they don't like Apple? Nothing breeds contempt like success.
5. Blu-ray. Optical storage, like Flash, is dying. Apple didn't pick a side in the HD-DVD vs Blu-ray "war". Some might call this realpolitik. Personally, I think they took a long term view that the winner was irrelevant. The well is drying up. Who controls it doesn't matter anymore.
6. Apple is by far the company that has demonstrated an utter devotion to the paramount importance of the user experience. Now you can disagree with some of the decisions they've made but, on the whole, no company has engendered quite the same loyalty and fervour that Apple has for good reason.
They're still at the mercy of the market as a whole.