That sucks!
I didn't have problems downloading it, but I did have problems installing it. My key kept getting rejected, then just decided to start working. It was odd.
I think it's rather interesting that they limit the number of times you can download the program...I mean, you need a key to install it, and while I know there are people out there who can get around software protection systems, I don't think FTM is high on the theft list. They should just make the software available to download unlimited number of times and require the key to open it like they do already.
I write software for a living myself, and trust me, frustrating your paying customers, even when it isn't the programming team's fault, comes back to haunt you. Enough problems and you lose the account. Ancestry.com (I would imagine) is a big account, enough complaints, and they move on.
I guess they have used NOVA for a while now though, and getting a new vendor for software is hard since NOVA probably holds the copyright to the source code. Ancestry.com would need to start something completely new, or if they own the copyright, take it away from NOVA and give it to someone else.
Just my 2¢ worth.
Good luck!