I was looking at the ordering page and salivating last night but it does not seem to mention anywhere on the site the kind of protection it uses?

It says it requires the DVD in the drive to play which is annoying enough but what about cd-keys? Online authentication like rfactor? Dongle? Anything?

And controls, will I be able to use my X-45 and Logitech momo pedals (for rudder) like I can in F4af?

It doesn't have copy protection, AFAIK.

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X-Plane (all versions) does a simple CD check as mentioned. If the CD/DVD is not found, the sim goes into 'shareware' mode, where the controls stop working after so long.

As for controllers... Just about anything with an axis and/or buttons works in X-plane, multiple controllers at once as well.