Douglas Maicon had given them the lead at half-time, but Claudio Pizarro equalised in the second half.
"I was not upset by the jeers. The public is always right and are the most important element in a football club, so for many years I have learned to respect their opinion," said Mourinho after the 1-1 draw.
"If we compare the goal we scored to the chances we created, obviously it seems disappointing, but we played dynamically and in an attacking fashion in the first half.
"Football can be difficult to analyse. Yesterday I saw Arsenal beat Porto 4-0, but in the opening half-hour Porto could've been 3-0 up. At the final whistle everyone thinks Arsenal played a spectacular game.
"What could've happened today had we gone into the break 2-0 up? Inter played a positive match and in my view you can't talk about a bad performance. If any team should've won this, it was Inter.
"Werder Bremen are a major side who are regulars in the Champions League and have been working with the same Coach for many years.
"I faced them with Chelsea a while back and they are still playing the same system with many of the same elements.
"We knew it was tough and we wanted to score in order to win the game, but Werder equalised and we reacted with confidence, as Inter are not worried or afraid."