Yes - it's quite common to see those kind of complaints. But I think if I were Waterstones, I'd say, "Look, we pay our staff very little. We've trimmed costs as much as we can. You, the broader publishing community, need us to exist and thrive. And yet our profits are still just a tiny sliver of overall turnover. If we gave you fatter margins, we'd just keel over and die."
So what that says, I think, is (a) that it's tough being a smaller publisher probably also (b) there are still too many books being published. It's not that I don't like the smaller books / presses, because I really do. It's more that the commercial case for those things is ever harder to make.