Asking why some hosts charge for sub domains is like asking why hosts charge a hosting fee at all.
Everyone has a business plan, and pricing structure so they can make a company a success - or at least they should.
For instance, we charge for sub domains if the site is a site of it's own, and has it's own IP. We offer free sub domains for people that have their own domain though too.
Yes, a sub domain is very simple to set up. However, so is any other hosting account. Why do you pay? It is your choice as a customer. You can either pay for a quality service provided by your host, or you have the choice and freedom to move to a free host and wait for a few days to infinity hoping for any kind of support. In hosting since 1997, I found that there is a price to pay for good tech support. Some companies cater to the customer that isn't going to loose his business if he can't get support - others, choose to have great support. Most times, you get what you pay for, with FEW exceptions.
Sub domains and domain accounts are no different in server resources used. In most cases now days, they come with e-mail, stats, and many of the features in your main hosting account.
Just because a group of bozo's started offering unlimited everything, including disk space, and bandwidth, a few years back, it seems like customers now days want everything for free, but demand excelent support and uptime too.
Let's face it. Great techs cost a great deal of money.
A host should charge according to the level of serice being provided, like quality servers, quality bandwidth through fiber optics, quality tech support, and more.
The more they offer the customer in peace of mind, or the more they cater to a business class customer, the more they should charge for the extras that slow things down.
Minor extras or major,, they all add up. That is why hosts charge for things you would assume should be free.
For instance: 5 or 6 years ago, is not a long time ago. However,, unlimited sub domains would have not come up on any forum, let alone be expected for free.
It is all in their business plan, and they have to make their company grow at a cost that they can afford. Perhaps they offer something else for free that others charge for?
Hopefully, you can find a host that offers what you want or need, at a price you like, and you site will prosper.
Best wishes,
Tim L