SAN FRANCISCO – Linebacker Patrick Willis is the paragon of politeness, a true Southern gentleman whose answers are invariably peppered with "sirs" and "ma'ms."

After Sunday's 30-21 loss to New England, however, Willis had a hard time snapping out of game mode and into locker-room decorum.

He sat at his locker and stared coldly into space for 10 minutes. He was the last player to leave the showers, and after dressing he declined to speak with reporters.

"I'm not talking to you. Sorry," said Willis, who had a game-high 18 tackles. "I'm not doing any interviews."

The middle linebacker had to have been distraught at what has become the 49ers' biggest weakness – the heart of their defense.

As was the case against Arizona, Willis and his teammates simply couldn't get off the field Sunday against Matt Cassel and the New England offense. Using a straightforward attack, the Patriots controlled the ball for nearly 40 minutes, including a 36-minute stretch between the second and third quarters during which New England scored 17 points while the 49ers couldn't muster a first down.

Defensively, the 49ers opened the game in their familiar "Big Sub" package, which calls for two linebackers and five defensive backs. New England's counter move was predictable.

Like each of the 49ers' previous opponents, they reacted by pounding the belly of the 49ers' defense.

Last week, the Saints ran Deuce McAllister up the gut. On Sunday, it was 220-pound Sammy Morris who got the call. After rushing no more than 10 times in New England's first three games, Morris had 16 carries for 63 yards against San Francisco.

Running backs Kevin Faulk, Laurence Maroney and LaMont Jordan also had their chances, and the Patriots finished with 144 rushing yards, well above their season average.

"They had the ball for far too long," linebacker Takeo Spikes said. "It's disappointing and frustrating. We have to give our offense more opportunities. You've got to give (the Patriots) credit – they just played better than us."

The 49ers' offense didn't help matters.

Quarterback J.T. O'Sullivan and his receivers got off to a quick start, scoring 14 points in the first quarter. The second touchdown came on perhaps their most efficient drive of the season, one that required only three plays to travel 58 yards before O'Sullivan found Isaac Bruce in the back of the end zone for a six-yard score with 5:25 left in the opening quarter.

At that point, however, the hot streak went cold.

The 49ers didn't get another first down until the beginning of the fourth quarter. And when the defense desperately needed a rest in the third quarter, O'Sullivan threw the second of his three interceptions when he locked onto Arnaz Battle on a slant pattern and didn't see safety Rodney Harrison lurking on the inside.

"I probably tried to squeeze it in there, but that's still a throw I make a lot," O'Sullivan said. "When I released it, I thought I was going to get it in there."

Coming off a blowout loss in New Orleans, the criticism was that the 49ers allowed too many sacks – six in that game – on O'Sullivan and didn't harass the opposing passer enough.

This time, O'Sullivan mostly had plenty of time to throw and was sacked only once. The defense also had success in getting after Cassel, sacking him five times.

Still, Cassel was able to methodically move the Patriots' offense.

New England punted only once from the second quarter on and converted 8 of 17 (47 percent) third-down opportunities. The 49ers, meanwhile, converted only one of nine (11 percent) of their third downs.

"(I know) how excited people get about sacks and how they think they're directly related to winning," 49ers coach Mike Nolan said. "That should give you a great example that it really isn't. To win is all about having more points than the other team. It gets down to staying on the field offensively on third down and getting off on defense."

Read Matthew Barrows' 49ers blog at www.sacbee.com/ninersblog.