I subscribe to the Sitepoint newsletters but was dismayed to find Craig Bucker's post, dated 19th November 2010, in an email dated 13th December 2011, inviting further comment.
The post is closed for comments; despite the email inviting further comment, which is a bit annoying, given the 'heated discussion' that appeared to erupt over the choice of storage engine.
I like InnoDB for it's FKs but then I am not running a demanding environment, where data access times are a problem.
I haven't read all the comments yet, there were some claims on speed and performance in both camps but no one appeared to query the underlying database design.
I perceive PHP to have a much lower entry bar than, say Perl or C++. This may allow for the introduction to MySQL and databases to people who don't realise they have to clean their user input.
If people haven't researched much about securing their web application, be it a simple form or something more complex, then might it be a good bet they probably don't know too much about what is reasonable in database design either? That would result in a number of people not even thinking about which storage engine they might need.
Surely the database design will have an effect on performance; part of the design brief should be to assess which dbms and, in the case of MySQL, which storage engine best answers the project's demands?