Sometimes the choice is an ignorant one. Choosing something based on popularity alone is one such choice. Choosing a CMS is a responsibility - the cms will have a responsibility to the it powers, the developers implementing it, the site administrators and, the site owner and the site visitors.
Doing something just because loads of other people do it is one of my biggest frustrations with people. It has lead to slavery, racism, sexism, wars, violence and genocide. You cannot assume that something is right just because others do it without repercussions.
Wordpress is used by those who are unaware of its serious and fundamental architecture problems. Wordpress is NOT used by those who are aware of them (eg me).
I use windows because I'm used to it. However, in recent years I have found it limiting in some respects so my servers deploy *nix systems. I would make a permanent switch to *nix but I don't know how to do the basic admin things that I've learned to do on windows - its a time and resources thing - i don't have the time to learn how to set up an email client on an ubuntu desktop...my time is better spent developing the software my company sells.
Which brings us full circle to CMSs. There are people who can develop sites in wordpress, although WP does not have the flexibility for my needs. People can develop in Joomla (they've spent time learning Joomla). There are people who can develop sites in drupal (using black magic and witchcraft) and there are people who can develop in MODx because that's what they know too.
Because each CMS takes a while to learn, people tend to stick with the first one they choose and persevere with it. I'd like to think that the original choice is made on some research, background info and suitability for purpose. MODx fits my needs 90% of the time; the others don't even come close to 10% of my needs. The choice is simple. The architecture may not be best practice, but it fits the implantation so IMO its ok.