Look, the reverse-engineering that has to go on to allow create emulators are in many cases, illegal.
Reverse engineering - is taking someone elses work (usually compiled code or similar) and looking at it to try and work out what it does for the purposes of copying the concepts and process - all be it in a different way.
In reality, its one of those things that companies would probably (and almost always DO) turn a blind eye to when the end product is a homebrew or non-profit making product, unless the free availability of such product is going to infringe heavily on their business interests.
A parallel would be taking a well-known song, working out all the instrumental parts, getting a band together and recording it, then releasing it (free or not) without the original author's permnission. You are still negating the many hours it took to write and originally record that son, even if you ARE putting your time into figuring it out and learning it etc. In reality again, many bands play covers at gigs, which in reality arn't strictly legal without the record companys permission.
The main difference with emulated consoles/computers is the same argument brought up again and again with roms - that most of the time, the system/games are no longer a going business concern, so the companies are not that bothered. It is when the emulated system takes away from the business of a company, and even makes COPIES of it's games playable on a totally different system that the companies get pissed off. And I dont blame them.
Im still of the opinion that emulating current commercially viable systems is wrong, and like charging for emulators only brings in heavy handed corporate lawyers.
A case in point is that of the Playstation emulator for the PC and Dreamcast - Bleem. That started out as freeware, but graduated into a very good, but charged-for product. Sony decided to sue the hell out of the company and shut it down.
What it boils down to is that if the authors decide to charge, they are charging for the research and development of another company. It's up to that company if they want to get pissed about it, but if they do, they're unlikely to lose an argument in court.
Emulators should stay as donationware if the authors want to stay from being pulled through the courts.