There is no question that the Qur'aan guides to the straight path and to the truth. This is one of its major goals. Yet, at the same time, although this guidance is perfect and preserved, it must be allowed to guide the reader. The Qur'aan must be given the opportunity to tell its reader what the straight path is. That is, the reader must approach the Qur'aan with, if one may use the expression, an "open mind." If the reader has already decided what is right and what is wrong, and is only looking to the Qur'aan to substantiate his views, then the Qur'aan will never give him the guidance it contains. Indeed, in that case, the Qur'aan would never be given that opportunity.
Unfortunately, it is the case with some readers of the Qur'aan who, instead of letting the Qur'aan speak for itself, have taken it upon themselves to speak for the Qur'aan. If it contains any passage that contradicts their preconceived notions of what is the truth, instead of accepting what the Qur'aan says, they simply try to reinterpret the Qur'aan in such a way that it is consistent with their beliefs and ideas. They do not realise that it is their thinking and beliefs that need to be changed or corrected according to the Qu'raan and not vice-versa. Allaah سبحانه و تعالى, Who revealed the Qur'aan, is not in need of their far-fetched interpretations. It (along with the Sunnah of the Prophet Muhammad صلى الله عليه وسلم of course) presents the truth in clear and plain language and it is simply up to the reader to accept what Allaah سبحانه و تعالى has said in the Qur'aan.
In the history of Islaam, one can see that the lack of allowing the Qur'aan to state what is true and what is false has been a major characteristic of the heretical and stray groups (ahlul-bida'). 
They approached the Qur'aan with preconceived notions and tried to force their opinions on the Qur'aan. 
Without a doubt, it can be stated that they did not turn to the Qur'aan for its guidance - since they had already decided what the truth is. They turned to it only trying to substantiate their views. A glaring example of this nature is the Mu'tazilah  who even attempted to change the wording of the Qur'aan because it was inconsistent with their preconceived beliefs. The Mu'tazilah, due to the supposedly "ingenious" theories they developed, did not believe in Allaah's سبحانه و تعالى attribute of speech. They have a length theory and proof that such an attribute is impossible for Allaah سبحانه و تعالى according according to their notion of Allaah. 
A Commentary of the Hadeeth: "You are unto me as Haaroon was unto Moosaa."
On the authrority of Sa'd Ibn Abi Waqqaas رضي الله عنه, that the Messenger of Allaah صلى الله عليه وسلم said to 'Ali Ibn Abi Taalib رضي الله عنه: "You are unto me as Haaroon was unto Moosaa, except that there will be no Prophet after me." 
The narration of Ahmad on the authority of Sa'eed Ibn al-Musayyib has it that 'Ali رضي الله عنه replied: "I am content, I am content!"
Ibn Sa'd narrates essentially the same story on the authority of al-Baraa' رضي الله عنه and Zayd Ibn Arqam رضي الله عنه, who reported that 'Ali's رضي الله عنه reply was, "Indeed, O Messenger of Allaah,' to which the Prophet صلى الله عليه وسلم said, "It is indeed so."
Shaykh Dr. 'Ali Muhammad as-Sallaabee writes,
It was narrated that Jaabir رضي الله عنه said, "I heard the Messenger of Allaah صلى الله عليه وسلم say: 'Islaam will continue to prevail during the time of twelve caliphs.' Then he said something that I did not understand, and I aksed my father: 'What did he say?' He said: 'All of them from Quraysh.'" 
According to other versions, he صلى الله عليه وسلم said: "This religion will continue to prevail and be strong during the times of twelve caliphs." 
"The peoples' affairs will continue to be prosperous during the reigns of twelve men." 
"This religion will continue to prevail until you have had twelve caliphs, under all of whom the Ummah will be inited." 
Dr. 'Ali Muhammad as-Sallabi writes,
It is indeed a great trial for a Muslim to make du'aa', sincerely and properly, continually, for a long period of time, and yet see no sign of response. Here, a person's eemaan in Allaah سبحانه و تعالى is truly tested. And here is the opportunity that Shaytaan uses to try to sow his whispers, and plant his doubts in a believer's heart. In this way a person might start thinking evil thoughts about his Creator, or start doubting the wisdom of the Divine Decree. So whoever falls into this, should immediately seek Allaah's سبحانه و تعالى refuge from Shaytaan, and turn to Allaah سبحانه و تعالى sincerely, making yet another du'aa' that he be saved from Shaytaan's evil plots, and that he be granted patience to withstand the test that he is undergoing. He should also ponder over his own limited knowledge and intelligence, and realise the infinite Knowledge of Allaah سبحانه و تعالى, and the extreme wisdom behind any Divine act.
The response to this question lies in understanding that the outcome of anything is dependent on the performance of the efforts that are necessary to procure it. In other words, it has already been decreed, for example, that a seed will give fruit if planted, but this will not occur unless the farmer takes the appropriate efforts in irrigating the crop, maintaining it, protecting the seedling as it grows, and ensuring as much as he can that the factors are amenable for the plant to give fruit. So even though a person believes in the Divine Decree, he must at the same time strive all he can to ensure that the desired goal occurs. So du'aa' is the means that one uses to achieve the desired goal that one has, and this means in no way contradicts the destiny that has been written for that person.