Safety of transfer between iPad and PC... Safety is not so much a matter of how you transfer (wired or wireless) vs. the safety of what you are transferring (does the file contain malware of some sort).
Files don't get infected in transit - they start out infected at the source, or they are infected once they arrive at their destination. (Well, outside of spy novel scenarios - anything's possible, it's a matter of whether you are likely to be the target of a sophisticated, expensive, incredibly rare kind of attack. I'm going to assume that you are not such a target, because if you were you would have paid security experts working for you.)
As to the safety of what you are transferring to your PC, it doesn't matter whether you are downloading the file directly to the PC using Firefox or other browser, or whether you are importing the file to the PC from the iPad using iTunes - the anti-virus software on your PC is responsible for scanning anything you import to your PC, regardless of the import method you use. (assuming you use anti-virus on your PC, which I presume you do, considering the concerns you've been voicing).