Legitimate programs can be incorrectly diagnosed as being malware because they somehow fit the heuristics of a particular AV.
This can be particularly true for system tools that need to be able to do "low level stuff".
Crypters try to tap into that market (as well) by adverising it as a means to circumvent anti virusses for the above case. And i've seen several legit programs use crypters for that specific purpose.
It's a non-ideal solution for various reasons.
If you really want to be safe from false positives of AV, then the best way to do that is by digital signature. Malware won't be doing this because it establishes a clear link as to who created the software, and thus also who's potentially liable for legal repercussion.