First, there are DPS benchmarks for even the utility classes. They are not as high as the pure classes, but they are there. For example, your Rogues may be putting out 2100 DPS on Teron Gorefiend, but your Enhancement Shaman is only doing 1600 DPS. This is okay. If your Rogues are doing 2100 DPS and your Enhancement Shaman is equally geared, but only doing 1200 DPS? That's a pretty good sign that they're doing something wrong. These numbers are never solid, and shift wildly with gear levels. Sometimes the hybrids will be very close to the pure classes, sometimes the gap will be massive. For more information on this sort of thing, I highly recommend lurking around on the Elitist Jerks forum. The place is full of good information.
Next, keep an eye on deaths. This may seem like a silly little detail, but it's true. All DPS classes are plagued with dumb deaths caused by wanting to squeeze out just a little more DPS time, but this is especially true of some of the lower DPS hybrids. Not everyone does this, but you'll see it pretty often. In an attempt to get in a little extra DPS time to compensate for their lower-than-average damage, a hybrid will start nuking away without a care in the world way before they should, or after they should have stopped. Dead hybrids not only means they do no damage, but it also means their utility is gone. This can severely hurt your raid over the course of a fight. If one or two people are consistently dying early, it's time to start troubleshooting. Are they DPSing too early? Do they not have enough Stamina to survive the environmental damage of an encounter? Are they focusing too much on damage, and not enough on using Healthstones/Potions/Etc?
Track the stats tied to the specific class/spec combination's utility. Does the Retribution Paladin have enough +Hit to keep all of the Judgements refreshing? What kind of heals is the Resto Druid casting? Are they using Lifebloom to its fullest potential? Are blessings getting rebuffed reliably? Does the Shadow Priest have a good uptime on Vampiric Touch? Most of these are things you can check just by looking at a WWS report. If you only have one Resto Druid in your raid, they shouldn't be chain-casting Healing Touch. While Dreamstate is technically an option, it isn't what you want your one Resto Druid doing. You can gauge their knowledge of their role just by looking at the breakdown of what spells they're casting. A good Restoration Druid won't be tops on the healing meters, but those HoTs are invaluable. They may not seem very important while you have them, but you'll notice them when they're gone. If you don't have them, you'll find that your raid goes much more smoothly when you get them.
I cannot stress enough the importance of watching that all utility is being used as much as it can be. If you have someone with Improved Faerie Fire in your raid and it isn't constantly on a boss, find out why. If a shaman doesn't have totems laid throughout the entirety of a boss fight, find out why. These are things that won't directly show up on a damage meter, but could make or break your raid. An Enhancement Shaman in the melee group not giving the Windfury Totem buff to their group is like your Protection Warrior trying to tank Illidan without a shield. Seeing that Warrior die horribly is hilarious the first time, but you probably aren't interested in it happening repeatedly. If your Shaman can't drop totems, that's an important part of the class and something that should be addressed.
Like with all raiders, the simple ability to adapt to new situations should be used to assess performance. This isn't something you'll strictly apply to hybrids, but an important detail nonetheless. Are these players fast/smart enough to not stand in giant pools of fire? Can they interrupt spells properly? Is the druid capable of shifting out of kitty, Innervating someone, and getting back to DPSing? Does your Enhancement Shaman know what Totem Twisting is, and does he/she do it? Are the healers capable of Decursing, Cleansing, and Healing in the thick of battle, or do they only have enough focus to tackle one of those tasks?
To sum up, a knowledge of the class you're assessing is needed to judge a hybrid's performance in a raid. Every raid leader or officer should have some understanding of the class they're assessing. A simple glance at the Damage Meter isn't going to tell you who's worthwhile and who isn't. You need to look a little deeper, know a little more. Dig around Elitist Jerks for the information you need. Utilize the tools available to you(such as WWS) to take a deeper look at the stats you want to know. Hybrids do take a little more brainwork for all involved, but the contribution of a good hybrid player is absolutely amazing.