Some thing it cites are still reasonably true, but others are complaints that reflect the Haskell of a different era. For example, it says, "Even more unfortunate, the applicative functors were introduced to Haskell's standard libraries only after monads and arrows, thus many types are instances of Monad and Arrow classes, but not as many are instances of Applicative." This has not been true for about half a decade, when Applicative was made a superclass of Monad. The article follows with: "There is no special syntax for applicative functors because it is hardly necessary." This is also no longer true, since the introduction of ApplicativeDo: even if you don't like it (and I confess I'm not a huge fan of ApplicativeDo myself!) it turns out that many people do find that sugar easier to write.
However, I think the key point I'd make is: all the advantages listed here of using monad without do-notation are real in some cases, but there's nothing stopping you from not using do-notation sporadically! Occasionally a snippet that uses do-notation can be made much clearer by using >>= or some other monadic function, and occasionally a snippet that uses >>= can be made much clearer by using do-notation, and I don't think there's anything inherently wrong with Haskell keeping both. To make a Python analogy: sometimes you can express a given construct more clearly with a loop than with a list comprehension, but I don't think that list comprehensions should be considered harmful: just use those tools when you need them, and don't use them when you don't need them!