Particularly in the context of the atheism/theism debate, there are valid reasons skepticism is usually justifiable. Here are just two quick ones:
1. Many religions permit only a top-down transfer of information, with extra-churchicular programs devoted to 'deeper understanding of the faith' for those with further questions. Contrast this to the Bereans described in the book of Acts, who are described as "more noble" for their habit of "checking the scriptures" to see if what was being preached to them was supported or not. This is a sort of "skepticism" prevalent amongst believers; not as much a skepticism over whether God exists or not as a skepticism over the statements from religious authorities. Essentially, the habit of questioning and fact-checking the pronouncements of religious authorities is applauded in scripture. (Acts 17:11)
2. Many individual adherents of the various faiths either do not, can not, or will not defend most or even any of their beliefs. Contrast this to Peter who admonishes believers to "always be prepared to give an answer to everyone who asks you to give the reason for the hope that you have." (1 Peter 3:15) Or the more obscure New Testament writer Jude: "Be merciful to those who doubt." (Jude 1:22) Not everyone can say their pastor or church conforms to these requirements, but these are requirements the Bible plainly states.
Since the shortcomings of so many religious institutions and believers fall into these and many other categories, is it any wonder people fond of reason often look upon the whole enterprise with an eye of suspicion?