Nit: If you're filing a flight plan, you do it with the country you're departing from. Even if you're piloting an aircraft departing into the US, it wouldn't have any effect on operations if you couldn't reach US websites. There's also several alternative ways for pilots to file flight plans outside of the web.

(The flight plans get passed between countries via AFTN/AMHS, which are dedicated telecommunications networks independent of the Internet.)

If a Govt decides that I am pretty sure they won't stop at anything but TLD level banning. Besides I don't know about other countries (or EU) but I won't be surprised if our giant industrious neighbour already has infrastructure in place just for such Trumpian shenanigans :)