Recently I saw a discussion of my entry on how ZFS scrubs don't really check the filesystem structure where someone thought that ZFS scrubs only protected you from the disk corrupting data at rest, for example due to sectors starting to fail ( here ). While ZFS scrubs have their limits, they do manage to check somewhat more than this.
To start with, ZFS scrubs check the end to end hardware path for reading all your data (and implicitly for writing it). There are a variety of ways that things in the hardware path can be unreliable; for example, you might have slowly failing drive cables that are marginal and sometimes give you errors on data reads (or worse, data writes). A ZFS scrub has some chance to detect this; if a ZFS scrub passes, you know that as of that point in time you can reliably read all your data from all your disks and that all the data was reliably written.
If a scrub passes, you also know that the disks haven't done anything obviously bad with your data. This can be important if you're doing operations that you consider somewhat exotic, such as telling SSDs to discard unused sectors . If you have ZFS send TRIM commands to a SSD and then your scrub passes, you know that the SSD didn't incorrectly discard some sectors that were actually used.
Related to this, if you do a ZFS level TRIM and then the scrub passes, you know that ZFS itself didn't send TRIM commands that told the SSD to discard sectors that were actually used. In general, if ZFS has a serious problem where it writes the wrong thing to the wrong place , a scrub will detect it (although the scrub can't fix it). Similarly, a scrub will detect if a disk itself corrupted the destination of a write (or a read), or if things were corrupted somewhere in the lower level software and hardware path of the write.
There are a variety of ZFS level bugs that could theoretically write the wrong thing to the wrong place, or do something that works out to the same effect. ZFS could have a bug in free space handling (so that it incorrectly thinks some in use sectors are free and overwrites them), or it could write too much or too little, or it could correctly allocate and write data but record the location of the data incorrectly in higher level data structures, or it could accidentally not do a write (for example, if it's supposed to write a duplicate copy of some data but forgets to actually issue the IO). ZFS scrubs can detect all of these issues under the right circumstances.
(To a limited extent a ZFS scrub also checks the high level metadata of filesystems and snapshots. since it has to traverse that metadata to find the object set for each dataset and similar things. Since a scrub just verifies checksums, this won't cross check dataset level metadata like information on how much data was written in each snapshot , or the space usage.)