Long lines like these (especially strings) should be broken along multiple lines.  Astropy also uses `.format()` for all strings rather than `%` formatting.  And although *I* like the wording, as it sounds more like what I might tell a user face to face, the wording of exceptions generally can and perhaps should be a bit more direct.  For example these line might be written:

```
                col_unit = input[col.name].unit
                try:
                    col.unit = col_unit.to_string(format='fits')
                except FitsScaleError:
                    raise FitsScaleError(
                        "The column {0} could not be stored in FITS format "
                        "due to having a dimensionless unit of {1!r} that "
                        "is not recognized by the FITS standard.  Please see "
                        "the documentation on dimensionless units: "
                        "http://astropy.readthedocs.org/en/latest/units/standard
_units.html#the-dimensionless-unit".format(col.name, str(col_unit)))
```

Here the last line goes over due to the long URI, but this is still better.