The Chicago Manual of Style has an interesting way to address this: they omit the apostrophe, unless there are periods in the abbreviation. So this would give you ATMs, or alternately A.T.M.'s. (A.T.M.s looks weird.) chicagomanualofstyle.org, "Plurals"
This page indicates that acronyms ending in the letter "S" get an apostrophe, something I've seen before, but can't find in a general reference. So one would write ATMs and SOS's.
A page on the North Carolina State University website (which no longer exists) referenced AP's rule as being to always use an apostrophe.
The 2009 AP Stylebook's "plurals" entry has no section on acronyms, but mentions "VIPs", I can't find anything addressing how to specifically pluralize acronyms. (The "abbreviations and acronyms" section is also of no help.)
Personally, I omit using apostrophes unless I can't avoid it. I do use them when talking about single letters or where it would avoid confusion. (For example, SOs for "Significant Others" looks like an incorrectly capitalized SOS.)
To paraphrase Carol Fisher Saller, the clearer usage is the correct one.
