I've built a PDF reader for the iPad and I've noticed some color problems when doing a side-by-side comparison of the document in preview verus the simulator and device.
The best way to describe it is to say that the colors have become more intense. Any discrepancies between similar colors used in close proximity have become more noticeable while all the colors seem brighter in general.
Despite the hype connecting the iPad to the print industry, it doesn't supply a device calibrated CMYK profile installed. As a result, any PDFs with CMYK content tend to look quite crazy. Conversely, I believe that it handles conversions from Adobe RGB to the iPad's screen very well indeed, so you'd be highly recommended to find a way to adjust how you're outputting your PDFs or to find a tool that can do a conversion after the fact.
I've dealt with this only from the implementation side so don't have direct experience, but I believe that at least in InDesign it's a simple export toggle.
When I wrote that I forgot to consider that the bitmap images I was using were EXPORTED for the web from Photoshop (i.e. save for web), and therefore by default, they displayed correctly. Looking at my print PDFs that have images embedded in them, I can see that any of them that use the wrong profile have high contrast and bad coloring in the images and the vector elements.
I suggest that for images you want to display on the iPad, that you try either exporting them for web, making sure that you have enough resolution to look good on the iPad, or else saving them with an RGB profile, either Adobe RGB or working sRGB - see which looks best.
Note that there is a difference between "assigning" a color profile and "converting" to a color profile, as one of them is "destructive" and degrades the image quality a bit when making the conversion, and the other is not. You might try both with your images - save a series with a combination of these 2 variables - which profile and which method to get there - and see what works best with your images.
I might do the experiment myself soon with different types of images and see what looks best on the iPad.
Keep in mind that sRGB profile was created for computer monitors and Adobe RGB 1998 is a good RGB profile for digital printing (and more), but the iPad is neither really - maybe soon there will be a profile created for it :). Since I haven't tested it in-depth I'd suggest you try both and see what turns out true-to-color for you.
There are a couple of good blogs I have seen about using Photoshop for iPhone & iPad design. This one seems to be in-depth. I plan on reading it soon:
When you use Pantone colors, they do not contain RGB definitions that are embedded within the document - they are, by default, for ptint. Therefore when you use Pantone or CMYK colors, if you do not export correctly they will be way off.
When you export your document from InDesign to a PDF, select the "Output" tab and choose "Convert to destination". Then set the destination to Adobr RGB 1998. Make sure that "Include destination profile" is selected.
Alternatly, change the color profile in Acrobat.
Normal computer monitors have a wider latitude and will display a range of color profiles in a way that is closer to the original, but the iPad is different. While bitmap files such as photos display properly, the color conversion in vector-based files is off.
I assume that the answer above that the iPad/iPhone "doesn't supply a device calibrated CMYK profile installed" is correct and that the reason is memory allocation & processing power - however that last part is a theory at this point.
Check your PDF source's Color Profile. If you intended to use it on iPad, sRGB or Apple RGB might be your friend.
Did you hold the device next to your monitor to compare it?
If that's the case, I'm not surprised. I'm working in the printing industry and color matching is an important factor there.
What they do is to calibrate their monitors and screens using external color measuring devices. These devices (in combination with some driver software) allow to calculate the needed compensation to let the screen/monitor show color in a way it's going to be printed on paper.
Unless you have such a device (to calibrate your screen to your iPad's screen), I doubt there is much you can do. The PDF is displayed by the underlying software in the same way as in your desktop machine, but the physical screen hardware works differently. Try the following: buy another monitor and compare it again. You'll see different results again.
So my suggestion here is: do not trust the Simulator. The simulator is just there to allow quick testing of your code to see if everything works roughly as expected. What counts is how it looks/works on the hardware device! So always tune your software so it works correctly on the device, not the simulator.
TL;DR: It's due to different screens displaying colors differently. Make it work on the device, ignore visuals in the Simulator. Users are using the device, not the Simulator; and the device is mostly the same everywhere.
Also, I saw that somebody mentioned image FORMAT in addition to color.
Although the iPad supports a few file types, if you were to develop an app you would NEED to provide .png images for the app. Also, if you take a screen shot from the iPad, it will supply you a .png file.
Since this is either an iPad-friendly or iPad-native format, I would suggest giving that a try.