I too have found that the iWork section of iCloud on my desktop will not accept PDF docs, which Apple has been saying it does. For example, this is from iCloud help, which I looked at today (6/3/12):
"Get documents stored on icloud.com
When you create a document on an iOS device (iPhone, iPad, or iPod touch) set up with iCloud, the document appears automatically on icloud.com/iwork and on your other iOS devices set up with iCloud. You can edit the document from any iOS device, and the document is immediately updated everywhere.
From icloud.com/iwork, you can also download the document to your Mac or Windows computer and edit it. You can then drag the edited document from your computer to icloud.com/iwork. The document is automatically updated on your iOS devices.
Supported file formats include Keynote ’09, Pages ’09, Numbers ’09, PowerPoint, Word, Excel, TXT, CSV, and PDF."
Well, that last line is clearly not true. As far as I can tell, iCloud/iWork will not accept pdf docs.
Can anyone, particularly from Apple, explain how you replaced MobileMe -- which happily accepted PDFs, an incredibly common document format -- with another service that doesn't? And if this is going to be fixed, when will it be fixed?
The short answer is that when it comes to iCloud, your documents are sectioned off into silos based on the app that is handling them. So since you're saving your PDF into Preview for Mac, the only app that can access those PDFs on iOS is Preview for iOS, which incidentally does not exist.
Ironically, Apple does make an iOS that saves PDFs to iCloud--iBooks. But iBooks is iBooks and Preview is Preview, and they don't talk to each other. So no iCloud sharing between them.
If you want to go the third party app route (but still use iCloud), the closest thing I've found is PDFPen. They make a Mac app and an iPad app, which they advertise as using iCloud. They don't make an iPhone app though, which may defeat the purpose of cloud document storage if you use you iPhone heavily.
So the question is, which will come first? Preview for iOS? iBooks for Mac? PDFPen for iPhone? Any of the above would finally bring "full" PDF iCloud support to the Apple ecosystem, where by "full" I mean accessible by an iPhone, iPad, and Mac.
I'm in the same position as a lot users who are asking for full iCloud PDF support: I use my iPhone, iPad, and Mac heavily and I need a single app that will save my PDFs to a common iCloud storage. First developer to get there gets all my money!
That's a great writeup by medstudent2015. Another option is to use something other than iCloud. A number of cloud storage services sync to your Mac, and are accessible via iOS apps (dropbox, google drive, etc.). Sugarsync looks interesting as it actually syncs the files between devices, including iOS. I stopped using it about 6+ months ago, as it was unreliable (the files on the devices didn't match), but perhaps it has improved, or only some folks had problems. I think Box is just cloud storage, without syncing to devices, including your Mac.
Similarly, for cloud storage that doesn't sync to the device, you can use an app (like GoodReader) that will reach into your cloud storage and pull down what you have stored there (GoodReader is for PDFs).