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"](https://web.archive.org/web/20111209141645/https://www.chicagomanualofstyle.org/CMS_FAQ/Plurals/Plurals11.html)

[This page](https://web.archive.org/web/20051207013915/http://www.jhsph.edu/publichealthnews/style_manual/a.html) 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 ([available on the Internet Archive](https://web.archive.org/web/20151015071159/http://www.ncsu.edu/ncsu/grammar/Apostro3.html)) 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](http://www.subversivecopyeditor.com/blog/), the clearer usage is the correct one.