I've liked it for some time now, and that preference has been driven purely by the nice clean uncluttered interface that they've always had. I'd say that their interface today is the most cluttered it's ever been. Which still makes it far cleaner an interface than it's competitors. Take a look at a couple of random selections from the same space, shown below. The pictures say it all.
I thought about my preference for the website, and I remembered that though I've always liked it, it's not been the site I've used for ALL my domestic travel (they only recently introduced international flights). I've occasionally used other websites when they've given me significantly cheaper offers. However, if all the prices are more or less closer, I'd rather use Cleartrip.
I also realised that they have a regularly updated, and interesting blog. I first stumbled upon it, when someone (sorry, but I forget who/where) linked to their 5-part story on how they developed their visual identity. I had used it as an example in a lecture of developing brand identities. The story starts here, and you can navigate from there on.
An aside. The one thing I always wondered, though is whether Cleartrip designed their interface page first, or whether it was Kayak. Their interfaces are visually similar. There is a discussion about that here (scroll down to the comments). Kayak, for it's clean interface, and nice functionality, has been my preference for international travel in the past. However, Cleartrip now has international flights, and Kayak has an indian site in beta. I'll let my emotional consumer decision making decide, at the moment, which one to use.
PS: for some reason, the images are getting all skewed when I'm uploading it, I'm trying to fix it.