She should make it bigger.

Assuming you mean project structure, exactly the same can be said of any program language, including Ruby, Python and JavaScript (and especially JavaScript). If you're a terrible programmer, you're going to program terribly in any language you choose.

Also, with an enforced structure comes inflexibility to do exactly what you want, surely?

The same can't be said for Ruby and Python so much because there are very clearly recommended choices for frameworks, that encourage good project structure.

JavaScript, well, that depends. There's plenty of good frameworks around for client-side JS, but like PHP, there's no apparent (to a beginner) need to use them, and it's simple to get results without them, especially if you use jQuery. This is, clearly, why there's so much terrible JS code around. If you're learning JS to use on the server, Express is probably the default framework recommendation, and at least nudges you towards keeping things organised. You say that like it's a bad thing. Beginners don't know enough to avoid the pitfalls, so some structure is helpful to keep them on the rails.

There's a steep learning curve that can be daunting and downright discouraging, so easy wins can be important. Also there's many tutorials and online stuff that present contradictory methods, and new versions, security patches &ct. keep coming out to obsolete 'accepted' methods. It's all a bit more complicated than you make it out to be.

But they're frameworks, they're not inherent of Python and Ruby. You have to seek those out to use them. Scratch that, you have to know you're looking for a framework in the first place before you even go looking for one. I'm pretty certain anyone starting out in Python or Ruby could write the same sort of really bad code as is possible in PHP just by following a few web tutorials and then expanding upon them.

If you want PHP frameworks to read about, have a look at Symfony 2 and Doctrine (an ORM for PHP), Laravel and Phalcon too and to a lesser extent (because it insists on still supporting PHP4) Codeigniter. PHP isn't the raw, brash scripting language it used to be, it has made huge leaps in encouraging interoperability in the last 3~4 years* especially through the PHP FIG and the PSR standards which are designed to make sure your code is interoperable with that of others.

* Trying to type the tilde, I've just found out my Girlfriend has changed my Keyboard layout to US English.

Well sure, nothing is ever as simple as it's usually made out to be, and I know how confusing a full framework can be at first (lots of new concepts you kind of need to understand before you can do anything), so it's nice to have what's basically a glorified templating language "just work" with no setup.

I understand, too, that most people don't even need a proper framework, that they just want to add a bit of dynamism to a few pages and aren't actually making a web app.

Why do I want to learn PHP and MySQL?

First, I'd like to be able to help with Beehive and it's development more in the future.

Another reason is most of the stuff we use is done in PHP and MySQL. So, I'd also like to know what I'm looking at when I'm poking around in them as well.

I'm not the sharpest tack in the pack, but I'm not too thick to learn either, and I do want to learn.  :-) I've already got HTML and CSS pretty pat. PHP and MySQL are next, then maybe I'll start on something else. We'll just have to see what happens.  :-)

Aye, I realise now why you'd want to learn, sorry :) Honestly, despite my general negativity towards PHP, it's still encouraging to see people willing to learn software development.

No worries and thanks!  :-)