Fabricate’s wording here is rather awkward; the original materials are both target and material component, are both converted into a finished product, per the rules of the spell, and consumed as part of the casting, per the rules for material components.
As written, you could actually argue that fabricate requires twice as much material as you need for the finished product, one to target and convert, and the other to use as material component and consume. If you accept this interpretation, then Ignore Components would eliminate the second set of materials needed for the component, but you would still need one set to target.
I’ve never heard of anyone running fabricate that way, and while I can almost buy it (fabricate is extremely powerful, after all; giving it a 100% up-charge might be better-balanced), ultimately if that were what was going on I would expect the spell rules to really explicitly indicate that. Like I said, no one seems to have come to that conclusion.
Which means that the consensus is that fabricate implicitly does some kind of weird conflation of target and material component. How that works is not spelled out by the rules, and is basically an unconscious houserule. Targets and material components are not normally the same thing and the rules don’t really specify what happens when they are—which means you could argue that yes, Ignore Components eliminates the need for the materials, which are both material component and target.
But I think a far more fair reading would say that even if Ignore Components eliminates the need for the material as material component, it does nothing for the need to target the materials, nor for the line that
Casting requires 1 round per 10 cubic feet (or 1 cubic foot) of material to be affected by the spell.
Ignore Components doesn’t touch that, and should still be in force even if the material component aspects of the spell are erased.
Thus, in conclusion, my answer would be “No, you cannot use fabricate to produce goods from thin air with the Ignore Components feat.”
I would also just comment that I do not think a balance-based argument here holds much merit: this is an epic feat we are talking about; balance does not exist in the epic rules, and so there is no particular reason to expect balance from them here.