As far as my experiences go, Squid Beakons can be put into two major categories: Last Resorts in case of TPKs, and Quick Saves when your team has pushed sufficiently into enemy territory.
The first category is because as long as my teammates and I have someone to jump to who's defending themselves well (preferably someone who's gotten the upper hand and splatted all nearby enemies first), we can easily get back on our feet and try to take the match back. In that case the Beakons only find use when all four of us get splatted and need to get back ASAP. Of course, I'm aware of the possible pitfalls in that category--Beakons placed where someone can easily destroy one when they see it, or an ambush waiting to happen there. Those mishaps along with the relative ease of reaching certain areas without (as
@LMG said) are probably a good reason many players might not trust or need the Beakons.
Quick Saves, on the other hand, usually happen when one team (either mine or theirs) has made a breakthrough into enemy territory (or the far end in Saltspray) and begins dominating the map. There, the guy with the Beakons will usually put them all over the furthest place possible at the enemy base. Should anyone get splatted while destroying the enemy team, they can just Super Jump back into the fray and have the Beakon guy do their thing again. It's especially effective in Saltspray; if someone gets well-placed Beakons onto the top area, their team can just come back to kick out the intruders so that the top half stays theirs.
Yet another reason that map might need an overhaul. In that case, you shouldn't have as much of a problem getting your teammates to get to the Beakons.
That's not to say Last Resorts are fruitless, however. I've heard some stories about how full teams respawning then getting to a Beakon in time made epic turnarounds and won. As long as you can convince your teammates that Beakons are preferable to jumping to you/swimming to action, you'll certainly get some mileage out of them!