AP sent an email to Media Matters and TPM, in an attempt at point by point rebuttal to their very carefully specified complaints. It appears, however, the author of the rebuttal either had not actually read the criticisms, or maybe thinks clearly documented facts don't matter.

Media Matters has posted the AP's rebuttal to the complaints by TPM and Media Matters, plus their surrebuttal.

Josh Marshall has responded as well.

update:
Paul Kiel at TPM Muckraker has posted his surrebuttal.