Yes, I suppose it is possible that 150 years in the future, mankind has mastered faster than life travel but opts not to use a composite in the windshield of a helicopter resilient enough to withstand a large piece of wood (maybe there's carbon fiber in the wood!!). It just seems odd. Especially when a puncture in the windshield has a fair chance of downing the vehicle what with the lethal gas it lets in and all.
Why would they worry about such an outdated type of weapon as a giant bow? People stopped worrying about bows centuries ago from our time, you design armor to stop a certain kind of weapon. You can design it to stop just about anything, but it is expensive, can rely on something that won't last too long (like a top level of armor that blows itself up to deflect shaped charges), and will likely be heavy as hell if it doesn't rely on something like the cage in Alex's picture or the reactive armor that blows itself up.
Enough glass to replace a small sedan's windows, and this won't even protect against shotgun slugs or 150-year-old big slow lead bullets, will weigh around 200 pounds, at least that is the ballpark I worked up a while back working on a story. I would predict that bullet-resistant glass will get heavier and more capable, but they will never design it to stop big relatively slow pieces of wood, they would design it with new tricks to be even better at stopping standard small arms fire, maybe up into small anti-materiel rounds, although by that point weaponry will probably have advanced as well. Assuming each of those arrows weighed five pounds (big damn arrows, as I remember, the smaller ones just bounced off the cockpit), and fired at 400 FPS, that has the energy of a .50 BMG bullet, but weighs 50 times as much. It's comparing a chisel to a battering ram. With a hard enough wood, I would not be the least bit surprised to see them penetrate the glass. Consider that the glass I keep mentioning is penetrated by soft lead bullets when copper-jacketed bullets barely crack it, I am confident that there are woods that could do it.
The humans didn't seem to adapt all that well to Pandora. They didn't adapt their personal armor to be effective against the small arrows, they didn't adapt their weapons to be effective against the local wildlife (if you can unload what is normally a mounted machinegun into the face of an animal without giving it pause, you need to get some bigger guns), and they didn't adapt their vehicles for combat against creatures limited to bows and arrows.