I am a novice in learning Quran. Just sharing my experience.
I think no one can claim and should not without examine it. Every believer of each religion should examine his own scripture to find the truth. One must not recieve/abandon his own religion without scrutiny. Thats blind following, disgrace for his own intelect.
Quran numerously invites its reader to examine the truths it presents. It will be clear only when one read it. It would be more clear when read it repeatedly and earnestly.
One more thing, clarity depends on the ability to discern also. There are some clear verses which are the foundation, as Quran informs us, which are also sufficient to be guided to straight path. But there are also some verses which need deep knowledge to understand. (3:7) These are also explained. But these are for the knowledgeable reader. Without special knowledge one can not even understand the theory of relativity, one of the most popular theorem of last century.
There must have many reasons- political, social, cultural even family traditions which clouded/persuaded the mind of people and made them misguided. This is easy. Even at the time of prophet (pbuh) it happend frequently. We generally think that each companion of the prophet (pbuh) was a true follower. This might not be the case. Many people embraced Islam or converted to protect themselves. There were many other interests also.
Some verses of Quran are time and space bound, I think. Such as 33:53. there are many others. Some verses are for exlusively for the prophet (pbuh) also. When it says, O believers! not necesarily it is a call for all the believers to come. If we read with context, I think it would be clear to us whether it is for the then believers or for every believers.
Quran must have a historical frame. But we dont need it to understand the Book. Those details could fullfill our curiosity, but God did not send the Quran as a history book or He sent not it to fullfill our curiosity also. Its a guide book.
Once again, after reading a few times now I think, Quran becomes clear to its earnest reader. It does not talk to just anyone.
Sorry for being so long.