The number being displayed for the cursor position is the character number, not the column number.
Observed behavior:
The issue can be easily demonstrated by using hard tabs instead of soft tabs:
Using spaces:

Using tabs:

Notice how the cursor after the tab character shows my position as "2". It's right, in a way -- I am at the second character on that line; but that doesn't give me any information on what column the cursor is on. Things get especially confusing when you reach the 80-character Preferred Line Length line, but the status bar shows that you're only on column 78 (or 75 (with two leading tabs), or 72...)
Expected behavior:
Most editors I've used do show the column number rather than the character number (respecting tabs as multi-column characters), and the setting for Cursor Position Format also says it should show the column number, not the character number:
Format for the cursor position status bar element, where %L is the line number and %C is the column number
Additional comments:
I think it would be nice to be able to use both character and column number in the format string (maybe add a %c for character number?), but that might be an enhancement for another day. At the very least, the existing column number value should be fixed to work with wide characters (such as the four-space tab character demonstrated above)
Tested (and screenshot) using:
Atom version: 1.10.2 (safe mode)
OS and version: Linux Mint 17.3
This same issue was reported back in January in the main atom issue tracker: atom/atom#10522