There's so much I dislike about Clerics I don't really know where to begin. Alot of my dislike of them comes from the fact that, unlike any other class, they are almost an absolute requirement to have in a party. A Druid can substitute somewhat, but usually can't cut it as the primary healer for a group.
The problem, at least as I see it, comes down to the core design of the game. Since clerical healing has always been assumed to be present in a party, the game was balanced around it. Characters will take alot of damage, but it's ok because there's supposed to be a Cleric there to patch them up. Imagine playing a difficult adventure without a healer at all and you will see exactly what I mean. Assuming you even survive a battle at all, you will suffer enormous amounts of downtime as you try to heal your injuries with rest. And some ailments can't be cured without magic - period (the chaos beast is a good example).
Some may think this turns out being good for Clerics. After all, they will always be welcome in a group. However, it also deligates a Cleric into the healing role. Many, if not most of his spells will be spent on healing. This usually leads to few people wanting to play the class, but again, since it's necessary for success, somebody has to. No other class is as important or inexpendable to a group. I've seen groups do just fine without a tank or arcane spellcaster or rogue. While every class brings something useful to the table, only the Cleric brings something that is vital.
So to try and "encourage" people to play Clerics, they made them the most overpowered class in the game. Let's just stop and compare them to the Wizard, for example. Most people would assume that the Wizard should be, if not the best, at least tied as the most powerful spellcaster, since their class is so single-mindedly devoted to that role and are terribly poor at everything else. Clerics not only have at least as good of spells as Wizards, they get more of them per day, including a bonus spell of each level which, unlike a Wizard, they don't have to give up anything to have. Clerics get to wear even heavy armor and cast spells in it. Clerics have a better attack bonus. They get two good saving throws compared to the Wizard's one. They get a d8 instead of d4 HD. And now with domains, Clerics can get access to some of the best Wizards spells as well. And to top it all off, Clerics learn every spell automatically and for free, while Wizards are stuck with the handicap of a spellbook and the enormous expense and chore of finding new spells. So not only are Clerics superior spellcasters, they are superior to Wizards in pretty much every other way as well. Thanks to their buffs they can outfight fighters. They can outcast Wizards. And they can heal. They can even cheat death, which IMO is one of the most anti-dramatic things about this game, but that is a rant for another time. Clerics used to at least have the drawback of having to serve a diety, but in 3.0 that restriction was also tossed to the wind.
But yet, despite this enormous carrot hung out in a desperate attempt to lure people into playing Clerics, I've known very, very few people who actually enjoy playing the class. To me, the Cleric class represents the worst of D&D. But since they are so ingrained into the system, since everything is balanced around their existence, I'm afraid that they are here to stay.