Theseus' ship is not a problem for materialistic explanations of anything; it's a problem for anybody who thinks the nature of a thing is governed by the words used to describe it.
The fact that you would continue to call a ship the same after exchanging all its parts is not an ontological problem, it is a problem arising from the imprecise use of language or intention to use an approximate/aggregate notion of identity. (I would recommend studying topology for a more modern understanding of this.)
And yet, consciousness is something that remains, regardless of whether we name it as such, and regardless of the specific cells that make up our brains. So it's as if it is the only thing that is not named 'by us' and yet remains 'something' independent of its makeup.
The fact that you would continue to call a ship the same after exchanging all its parts is not an ontological problem, it is a problem arising from the imprecise use of language or intention to use an approximate/aggregate notion of identity. (I would recommend studying topology for a more modern understanding of this.)