To be honest, I cannot see the connection, but that doesn't neccesarily mean that Bethesda were wrong to challenge the usage. The problem is that Legal Departments, and particuarly Lawyers that are bought in on a per-case basis, are interest in generating income, whether that be through payouts or court-fees.
When Mojang offered to surrender up the copyright, that should have been it, all that really should have been required between parties was an understanding that the two products were not linked intentionally or unintentionally.
I remember there was a gane called 'Pirates of The Caribbean', which was nothing whatsoever to do with the film and was, in fact, a re-release of an earlier game called 'Sea Dogs 2' that had been re-packaged to cash in on the Film market. That was actually authorised by Universal iirc, but it's that sort of thing that I would call unacceptable use of a name.