Keep in mind that in the studio and live (but especially in the studio), there is a ton of PEQ applied to real amps/cabs. A lot. And since the AxeFx is designed to emulate real world amps/cabs/mics, why wouldn't it be any different?
I think it's a good idea for all guitarists, especially those here who are using the AxeFx to handle all the amp/cab/micing duties, to read up on music engineering and production. It gives one an insight on how guitar is recorded and edited to fit in the mix. The tools to do that are all in the AxeFX, you just got to learn how to use them. So many people feel that EQ is an evil device that should never be used. If that were the case, then pretty much every well respected studio and live sound engineer would be "wrong" and I'm sure that's not the case. Instead, we should embrace these tools and learn how to use them properly to enhance our sound. Here's a great ebook that I recently read that has a lot of great how to's for guitar processing:
SYSTEMATIC PRODUCTIONS - Official Website - Mixing Guide
It's not free, costs $20 AUD, which is about $20 here in the USA. I think it's worth every penny (no I'm not affiliated with the author in any way, I just like the book). The book gives a lot of great insights on how to use compression, EQ, etc on guitar.
Long story short, I don't think having to use EQ is a bad thing. In real life you can't expect to throw a mic in front of a cab and expect it to sound perfect without any tweaking (EQ). And since an IR is supposed to be an accurate representation of a real speaker/cab through a mic, I don't see why it would be any different than real life. The AxeFx gives us all the tools we need to tweak our sound. Might as well use them!