He's not saying deny him all loot. And sometimes it's not about who wants what. BiS items are better served to

In the interest of guild progression, it's beneficial for more active members to be more geared. DKP (or my personal favorite, EPGP) take this into account, whereas /roll doesn't. Everyone is able to get gear, but if your core team isn't getting anything because of terrible rolls, and the folks who only show up once in a blue moon are getting it, then the guild is alot more likely to hit a gearcheck and get stuck.

Gearing up active members, or at least using a loot system which takes effort into account = better geared progression team = faster and more abundant boss kills = more loot for all.

And in regards to "If that's the case what's his incentive to run the raid if he knows he can't get any upgrades unless he is as well loved, or has a schedule that makes him just as available as tank 1 and 2"....Use a system with some balance, such as epgp. Who gets loot is a ratio of effort in and gear out. So even if he doesn't raid often, he's able to get some loot, without ignoring the fact that tank 1 and 2 there do alot more of the work.

Loot drama will always happen, but a fair, non randomized loot system can help.