The questions that you raise is of course what I am interested in discussing. I can't think of any way that PGP/GPG protects you against keyloggers or a pre-infected computer. I agree that they are relevant threats but my question is if it's up really to the developers to prevent rogue JavaScript in third party software and user's localhost. The same threats can be applied on all existing cryptosystems, as for with one-time pads where someone could look you over the shoulder - but that itself is not considered to break the underlying strength of the design. Or another example, how does Enigmail for Thunderbird protect you against having code injected and keys stolen? I don't think it does, but Enigmail isn't considered insecure. I think the questions are fair to raise but I see them raised far more often when people confront new ideas in comparasion to established practice, which I truthfully consider is a bit unfair judgement.

One of the factors which can narrow the scope of attackers is to use products like crypto stick, but then again what is preventing a computer from being rootkitted and having it's keys stolen as soon as they are exposed in the system?

Developers can of course only address weaknesses in what they have control over. We can't stop your computer from being infected by neither rootkits nor rogue JavaScript from plugins that you have volontarily installed. My advice would be to be careful and audit everything that may be a threat in order to at least try and minimize the risks. Unfortunately I don't think many users do that but it's not something we as developers can address and prevent.

The dilemma here is the same as with filesharing: if it's accessible it can be copied and transferred. There's no patch against that.