I've seen this question (and variations on it) a lot lately. What amazes me is how often people respond, but how few answer.
I have my preferences (I enjoy both stacks), but this is where most "answers" start to go wrong. It shouldn't be about what I want (or what anybody else wants).
Here's how I'd go about determining the value of MonoTouch - I can't be objective, obviously, but I think this is pretty zealotry-free:
Is this for fun or business? If you wanted to get into consulting in this area, you could make your $399 back very quickly.
Do you want to learn the platform inside-out, or do you "just" want to write apps for it?
Do you like .Net enough that using a different dev stack would take the fun out of it for you? Again, I like both stacks (Apple and Mono), but for me MonoTouch makes the experience that much more fun. I haven't stopped using Apple's tools, but that's mainly because I really do enjoy both stacks. I love the iPhone, and I love .Net. In that case, for me, MonoTouch was a no-brainer.
Do you feel comfortable working with C? I don't mean Objective-C, but C - it matters because Objective-C is C. It's a nice, fancy, friendly OO version, but if pointers give you the heebie-jeebies, MonoTouch is your friend. And don't listen to the naysayers who think you're a dev wuss if it happens that you don't like pointers (or C, etc.). I used to walk around with a copy of the IBM ROM BIOS Pocket Reference, and when I was writing assembly and forcing my computer into funny video modes and writing my own font rendering bits for them and (admittedly trashy) windowing systems, I didn't think the QuickBasic devs were wusses. I was a QuickBasic dev (in addition to the rest). Never give in to nerd machismo. If you don't like C, and if you don't like pointers, and if you want to stay as far away from manual memory management as possible (and, to be fair, it's not bad at all in ObjC), then... MonoTouch. And don't take any guff for it.
Would you like to target users or businesses? It doesn't matter much to me, but there are still people out there on Edge, and the fact is: you can create a far smaller download package if you use Apple's stack. I've been playing around with MonoTouch, and I have a decent little app going that, once compressed, gets down to about 2.7 MB (when submitting your app for distribution, you zip it - when apps are downloaded from the store, they're zipped - so when figuring out if your app is going to come in under the 10MB OTA limit, zip the sucker first - you WILL be pleasantly surprised with MonoTouch). But, MT happiness aside, half a meg vs. nearly three (for example) is something that might be important to you if you're targeting end users. If you're thinking of enterprise work, a few MB won't matter at all. And, just to be clear - I'm going to be submitting a MT-based app to the store soonishly, and I have no problem whatsoever with the size. Doesn't bother me at all. But if that's something that would concern you, then Apple's stack wins this one.
Doing any XML work? MonoTouch. Period.
String manipulation? Date manipulation? A million other little things we've gotten used to with .Net's everything-AND-the-kitchen-sink frameworks? MonoTouch.
Web services? MonoTouch.
Syntactically, they both have their advantages. Objective-C tends to be more verbose where you have to write it. You'll find yourself writing code with C# you wouldn't have to write with ObjC, but it goes both ways. This particular topic could fill a book. I prefer C# syntax, but after getting over my initial this-is-otherworldly reaction to Objective-C, I've learned to enjoy it quite a bit. I make fun of it a bit in talks (it is weird for devs who're used to C#/Java/etc.), but the truth is that I have an Objective-C shaped spot in my heart that makes me happy.
Do you plan to use Interface Builder? Because, even in this early version, I find myself doing far less work to build my UIs with IB and then using them in code. It feels like entire steps are missing from the Objective-C/IB way of doing things, and I'm pretty sure it's because entire steps are missing from the Objective-C/IB way of doing things. So far, and I don't think I've sufficiently tested, but so far, MonoTouch is the winner here for how much less work you have to do.
Do you think it's fun to learn new languages and platforms? If so, the iPhone has a lot to offer, and Apple's stack will likely get you out of your comfort-zone - which, for some devs, is fun (Hi - I'm one of those devs - I joke about it and give Apple a hard time, but I've had a lot of fun learning iPhone development through Apple's tools).
There are so many things to consider. Value is so abstract. If we're talking about cost and whether it's worth it, the answer comes down to my first bullet item: if this is for business, and if you can get the work, you'll make your money right back.
So... that's about as objective as I can be. This is a short list of what you might ask yourself, but it's a starting point.
Personally (let's drop the objectivity for a moment), I love and use both. And I'm glad I learned the Apple stack first. It was easier for me to get up and running with MonoTouch when I already knew my way around Apple's world. As others have said, you're still going to be working with CocoaTouch - it's just going to be in a .Net-ized environment.
But there's more than that. The people who haven't used MonoTouch tend to stop there - "It's a wrapper blah blah blah" - that's not MonoTouch.
MonoTouch gives you access to what CocoaTouch has to offer while also giving you access to what (a subset of) .Net has to offer, an IDE some people feel more comfortable with (I'm one of them), better integration with Interface Builder, and although you don't get to completely forget about memory-management, you get a nice degree of leeway.
If you aren't sure, grab Apple's stack (it's free), and grab the MonoTouch eval stack (it's free). Until you join Apple's dev program, both will only run against the simulator, but that's enough to help you figure out if you vastly prefer one to the other, and possible whether MonoTouch is, for you, worth the $399.
And don't listen to the zealots - they tend to be the ones who haven't used the technology they're railing against :)