From taking SOR:
(A few references taken out of Cambridge Studies of Religion, due to my memories being cloudy on the topic)
The negative connotations of the word "Jihad" in Muslim culture (or, depending on how you perceive it, "Muslim" culture) can be defined by first acknowledging a split in two types of Jihad. We refer to them as the Greater Jihad, and the Lesser Jihad.
Note, that the term Jihad appears as a supposed 6th pillar of faith. Core to every Muslim's belief, however, are 5. We shall not discuss them here for now.
In very broad terms, the Greater Jihad focuses on adding positives to within their own Muslim life. One may say, it is an intention to live their lives to the best of their ability. This may include Qu'ran study, working for social justice and simple acts such as forgiveness.
The Lesser Jihad, on the other hand, refers more to ridding the world of evil. Whilst it may seem natural to state that a devout Muslim (note, the religion is INTENDED to be PEACEFUL) would want to confront the evil in the world, this is the main thing relevant to misjudgement of acts and thus, the scars placed on the word.
As demonstrated in certain 'Muslim' parties (note: the specific group I talk about are not true Muslims in my eyes), the definition of Lesser Jihad becomes seemingly allowing for the execution of violence and warfare. Effectively, this assumes that killing is morally just, if it is with the intention to eliminate evil.
(One may question, then, how these certain parties are viewing "evil" in their eyes? Because when Muslims are tagged with the word "jihadist" in contemporary society, it's now referred to the groups that seek to kill for their own reasons. The advent of terrorism in 9-11 does indeed reflect the deal with Bin-Laden's actions - there is a story behind his ways.)
Just like words such as "gay" have come to refer to homosexuality, "jihad" has now come to refer to a specific bunch, who in my opinion, taint the Muslim community with actions they normally forbid, due to their own misjudged view of the world.