This has come up in one of the campaign I currently run. Comprehend languages, like most spells, has a limited duration and is therefore only useful as long as:

You don’t encounter more than one piece of foreign-language text over the course of the day.
The foreign-languages you do encounter can be completely interpreted before the duration runs out.

Of course, players could prepare the spell more than once, but then they find themselves short on spell slots. Charged magic items can offset the disadvantage of spells without requiring slots, but they tend to have a worryingly large up-front cost for a non-guaranteed payoff.

The problem with translation spells is exacerbated by the fact that memories are rarely perfect: A wizard who read the riddle-poem of Llasynt the Long-winded probably won’t remember it word for word, and if guessing the password for Llasynt’s front door requires the third verb in the fourth insulting stanza, then he’d better have made some detailed notes…

On top of that, comprehend languages does what it says on the tin: It allows you to comprehend written or spoken languages, but doesn’t allow you to speak or write those languages, making it useless if your cunning plan depends on asking a dryad where her bathroom is.

Linguistics, on the other hand is always on, is non-magical (and therefore works in situations where magic would be impossible, inadvisable or a social faux pas), and makes you a hit at parties. It also doesn’t require you to touch the target for it to work, which again may allow you to avoid potential hazards, inconvenient distances, and more social faux pas. Plus, it grants you an additional language known with each rank, which is a nice way to avoid making mistakes with the skill entirely.