First of all, there isn't a single character or position in the show that isn't lampooned constantly. Is Ned Flanders presented as square? Yes. Is he also presented as the epitomy of Christian patience and love, with children who are far happier and better adjusted than, say, the Simpson kids? Also yes. Given the show's nature, I can't see it being more "fair" to Christians than it already is.
As for Lovejoy, frankly, I've known too many pastors who fit his model not to laugh sadly when he's on the screen.
The Simpsons present religious faith as good, organized religion as not so much. As I've tried to find a church to settle in, I've found myself agreeing with that model more and more.
(Note: I did finally find a suitable church a few weeks ago, but it only has about 30 people, so I'm not sure that disproves my point.)
This song came from last season's Simpsons show, "Dude, Where's My Ranch?" and was nominated for an Emmy Award.
Everyone Hates Ned Flanders
Homer: Everybody in the USA,
Hates their stupid neighbor,
He's Flanders and he's really, really lame...
Flanders tried to wreck my song,
His views on birth control are wrong,
I hate his guts and Flanders is his name.
Lenny/Carl/Homer: F-L-A-N-R-D-S,
Homer: He's the man that I hate best,
I'd like to see his house go up in flames.
Lenny/Carl: F-L-A,
Homer: His name is Ned!
Lenny/Carl: E-R-S,
Homer: That's a stupid name!
He's worse than Frankenstein or Dr. No.
Byrne: You can't upset him even slightly,
He just smiles and nods politely,
Then goes home and worships nightly,
His Leftorium, is an emporium, of woe!
Lenny/Carl: F-L-A,
Homer: Don't yell at Ned!
Lenny/Carl: D-E-R,
Homer: His wife is dead!
Everybody hates that stupid jerk!
Byrne: Springfield rocks with Homer's joyous loathing,
Filling clubs with angry Valentinos,
You don't have to move your feet,
Just hate Flanders to the disco beat.
Homer/Byrne: He's your perky, peppy, nightmare neighborino!
If you despise polite left-handers,
Homer/Byrne/Flanders: Then I doubt you'll like Ned Flanders
Or his creepy little offspring, Rod and Todd.
Todd: That's us!
Rod: Hooray!
Audience: F-L-A,
Apu: His name is Ned,
Audience: E-R-S,
Apu: He is so white bread,
Choir: A smiley, moustache geek who walks with God!
Now, I am sure that after this song was sung, there was some sort of epiphany that led people to view Flanders in a more positive light at the end of the half hour. However, the choice is mine as to whether I think the show is good enough to stick around long enough to find out if that's the case, or if, as in the episode in which seems brothels were lauded as vital to every community, the moral would turn out to be murky, or even amoral.