Why be Agnostic or Why Science cannot explain everything

For a long time in my life, I have been a staunch believer in god, then I entered a stage of being Atheistic... Off-late I find Agnosticism a better way of explaining this world..
Being a believer, you tend to ignore many contradictions in whatever you follow. You also believe that some divine source is in control of your life rather than you yourselves..
In contrast, Atheists believe that they are entirely in control and all actions can be rationally explained.. All along my being Atheistic, I encountered a fundamental problem in explaining my stand, though I was never questioned along those lines by any of the believers around me.. I could never a very fundamental question which no science could explain or for that matter even question, that being, Why was there matter in the first place?? Forget Big bang theory, forget origins of life, black holes, anti-matter, universe etc,. which all seem to have some scientific explanation readily available. My question is even more fundamental and trivial, why was there matter and why was it structured in such a way and who put matter or created it in the first place. This is where I find being agnostic a much better proposition..
Being Agnostic, I could take my mind of these fundamental questions which have wreaked havoc with my being Atheistic. Now I can let science explain all that it can explain about my world and leave the fundamental questions which cannot be answered by science in the realm of an unexplainable source of creation and philosophy.

The fallacy of Heaven and Hell

Most religions around the world have a conception of Heaven and Hell after death. Christianity have Heaven and Hell; Islam has Jannat and Jahannam; Hinduism has Swarg and Narak etc.. Entry into Heaven is based on how good you have been in your life on earth. Those who fail to clear the cut-off are automatically relegated into Hell.
However, I fail to understand the very essence of this conception and our craving to be Heaven.. Humans, as also other species are strictly concerned with survival and fear death the most.. Once we are dead what greater fear can exist?? Whether you are in Heaven or Hell makes no big difference as you know that you are dead which is any beings worst  and ultimately only fear..
Off late clerics have advocated destruction and death to non-conformists as an easy access to Heaven/Jannat/Swarg.. But if you understand that Heaven/Hell make no big difference you understand the irrationality of man made death and destruction in the name of religion..