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With IOS, Apple wanted to get away from a traditional file system. They thought it was archaic. Their idea was that each application would contain its own files. For example, you would go to iBooks and see all of your books, but only books and no other type of files/data. Consistently, multi-tasking is one of the weakest areas on the iPad (iPhone).
Its improved in IOS 5.x, but just a few months ago if you tried to go to a web page and download a file, you couldn't reopen it in its destination program with a few exceptions. So, if you need to get something onto an IOS device they try to force you through iTunes. Some applications have a back-door through dropbox, but its not universal.
As to Calibre's complexity, yes it is. In other words, it is very full featured. Getting started is simple, but it can do a lot of extra things and understanding how to make it and its plugins do everything they offer may take some time. Especially since each target environment (iPad, Kindle NT, Kindle Touch, ...) supports different things. It is a bit like MS Word being complex. It's pretty simple to open up a page and begin typing. However, the level of complexity increases when you want to use features such as styles, mail-merge, or even macro-programming.
If your only goal with calibre is to transfer doc's to your iDevice, you really don't need calibre. It's strength is in maintaining a library/database of your books, in personalizing your books meta-data (such as titles and tags), and finally in converting between formats. Unfortunately, as you found out .doc files aren't really ebook files and can't be easily converted as such.
Good luck!
p.s. It may seem that some of the folks here reacted a bit strongly. You need to understand that Calibre is donation-ware. That means that a lot of folks offer payback in terms of gratitude for the work. They are more thankful for what it does offer than any upset over any shortcomings. They (we) certainly don't want to de-motivate the developers who (probably) earn much less for all of their efforts than they are worth. Any defensiveness is not directed at you, but is support for all of the work that is done on this excellent tool.
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