That doesn't matter at all. First, there's always some obscure Linux tool with the same name, simply because Linux has a long history, and good names are the on

That doesn't matter at all. First, there's always some obscure Linux tool with the same name, simply because Linux has a long history, and good names are the ones taken first, even when they're totally unrelated to their task (gnome, thunderbird, apt, to mention a few). Second, the name will not confuse anybody. 99.99% of the target audience will not have heard of the linux tool, and the ones that have will not thing "zsync.com, I bet that's going to be a site about diff transfers optimized for network load".