Ironically, Rails was specifically designed to minimize the kinds of problems the article talks about. And they did a heroic job. "Convention over configuration" are words to live by. Probably the single biggest idea in software architecture which was developed since I left high school.
But alas, there is STILL endless amounts of arbitrary, unpredictable stuff--like cr vs cr-lf, which has to be learned.
This has nothing to do with Rails.
In general, software is not easy. I think all on HN would know that.
Those who say they had built so-and-so over the weekend or in a week etc, it is great for them. But it sets some unrealistic expectations for the naive and those who are new to software development.