If this is sincere, then good:

An
Iraqi journalist arrested after throwing his shoes at George Bush, the
US president, has reportedly sent a letter to the Iraqi prime minister
to apologise for the incident and seek a pardon.

A spokesman for Nuri al-Maliki, Iraq’s prime minister, said on
Thursday that Muntazer al-Zaidi had acknowledged his shoe-throwing
during a news conference in Baghdad as “an ugly act”.

Yasin
Majeed, al-Maliki’s media adviser, told the Reuters news agency that
“al-Zaidi said in his letter that his big ugly act cannot be excused”.

According to Majeed, al-Zaidi asked the prime minister to recall the
kindness al-Maliki showed him during a 2005 interview when he invited
the journalist to his home.

“I appeal to your fatherly feelings to forgive me,” al-Zaidi was quoted as saying by Majeed.

[…]

However, Dhargham al-Zaidi, the journalist’s brother, questioned whether the statement was genuine.

Of course, he is being held by the Maliki government, so it’s equally likely he’s been roughed up, in which case this is just making the whole thing worse (and kind of proving his point in throwing the shoes in the first place, actually).

UPDATE: Yes, looks like he was beaten while in captivity, quite severely. As Thabet at Talk Islam wryly observes, “Under Saddam he would have been killed. Under the Newly Liberated Government Of Iraq, he ‘only’ gets a beating. At least that’s progress.” No wonder al-Zaidi is an instant hero to the Arab world.