The Messilas Yesharim teaches that the most harmful middah is leitzanus - scorn, ridicule, mockery and cynicism. A leitz can never grow because he is always looking to ridicule. In fact the nation that is the personification of evil on earth, Amalek, is called a "leitz" by chazal. Leitzanus is evil.
The internet is filled with leitzem. Their tortured souls can find no rest until they mock what is holy to the Jewish people. The chumash, the gemara, the medrash, tzaddikim, halacha, even G-d Himself - everything is fair play. The goal - to mock, to belittle, to insult and to degrade. The result - nothing is holy, so now I can do and say whatever I want.
My answer - If you have questions and difficulties with certain parts of our tradition you are in good company. Moshe Rabbeinu had questions on Hashem and every scholar since his time has been trying to understand to the best of his capability. We ask - but with respect and an abundance of humility. So the skeptic's job is to learn. Study the Tanach in depth, gemara, medrash, moreh nevuchim, emunos vi'deos, kuzari, sefer ha'ikkarim, mahral, ramchal etc. etc. They also had questions and worked hard to answer them. I have yet to meet an apikorus who has made a serious study of Torah with a desire to reach truth [although he might exist and I just haven't met him]. Most heretics are too busy either mocking religion or watching monday night football to study seriously.
Remember, if one is devoid of spirituality he is nothing more than a monkey with a laptop and a blackberry [to paraphrase the Rambam]. We readers of Mevakesh are trying to spread light on an internet so filled with darkness.
Love and blessings.