As for the first question, it varies with different churches, church leadership's familiarity with the fraternity, as well as religious views. It really does vary. Out of every church I've ever attended (about a dozen over my life span and probably 3-4 since I've been a mason as I've been trying to find one in my area), I've yet to have anybody give me grief over being a mason.
As for the Second question, the bible does not say anything explicitly about freemasonry. Often you will hear that men are putting more time/effort/devotion into freemasonry than into church and thereby makes it anti-church. To that, I say that any hobby or interest can replace church if the man does not place the proper importance upon church in his life. This argument usually is from specific examples from within their church, not as a whole.
Now as for the third question. The bible does specifically say "thou shalt have no other gods before me." (Ex 20:3) This verse it often cited against freemasonry. Freemasonry is NOT a religious institution and is rather *tolerant" of other religions. It does not condone one over the other. This is usually mistaken to mean that it somehow extols all religions to be true/equal/right/whatever. Rather, I prefer to explain it thusly: freemasonry is a fraternity that teaches morality to men by spiritual (not necessarily religious) principals. Since we do not discriminate other religions and believe that we can unite all men together, freemasonry rather tries to find a sort of "spiritual common denominator" that men of varying religions can identify with to, basically, get the point across. You can see how some church sects might take offense that we do not take a stance that THIS or THAT religion is the one true one and that we practice tolerance. I like to think that the argument that the church poo poos on freemasonry because it says all Gods/religions are the same stems from being simply misinformed about the fraternity.
EDIT: I would like to inject one further opinion based on observation and it is likely a controversial one... I firmly believe that if a man is not firm in what his religious beliefs are that he may get confused by freemasonry by the very fact that we practice such tolerance. The topics of theosophy and comparative religion could perhaps lead one to believe that multiple religions or deism is being taught as a dogma rather than getting the man to see a common thread in varying religions and take away from it the moral principle rather than a specific religious ideal. I too am a Christian (Baptist, but attend a non-dom church) and believe in God as well as my specific religious views. In studying the deeper masonic philosophy (well really ANY school of philosophy), you must study appropriately and synthesize the information rather than replace your foundational views with the author's.