It's easy to focus on BSG's daddy issues, what with Papadama and his all-consuming Adama Family Drama. (See also: Dee's last fight with her father, Kara and her deadbeat dad, Cavil as Evil Cylon Father, Tigh and Liam, Baltar and humanity...) But let's look at the mothers for a minute.
Socrata Thrace
What kind of mother she is: Horrible and abusive even if she does love Kara
Goals: Prepare daughter Kara for her Special Destiny
Status: Dead
Caroline/CarolAnne Adama
What kind of mother she is: Abusive alcoholic
Goals: none that we know of
Status: Dead
Cally Tyrol
What kind of mother she is: post-partum depressed; tries to kill baby along with herself
Goals: when happy nuclear family fails, turns to murder-suicide
Status: Dead and frozen
Sharon Agathon
What kind of mother she is: cares about daughter above everything; willing to betray every Cylon and human and ignore principles entirely if necessary to be with Hera; devotion to husband seems to be side-effect of him being father of her baby
Goals: Raise daughter Hera
Status: Alive (until 150k year time jump)
Hera
What kind of mother she is: We have no idea, since she's a baby throughout the series, so all we know is that she reproduces - apparently that's the only important point
Goals: her destiny is to reproduce, though we don't know what she wants
Status: Alive at series end (still a very young child) until the 150k time jump; then shown as skeleton
Laura Roslin
What kind of mother she is: symbolic Fleet Mom to match Adama's Fleet Dad; ruthlessly focused on survival of her "children" (but can be caring mentor - see Billy Keikeya)
Goals: Keep all 49,000 kids alive and find them a new home on Earth
Status: Spends whole series fighting her impending death to accomplish goal (except for VERY brief jogging-and-romance distraction), then once it is accomplished, dies
Caprica Six
What kind of mother she is: Starts series as baby-killer; major part of character development involves learning to love and want babies (gives up her freedom to protect Hera, thrilled when almost has own baby, great destiny fulfilled when protects Hera for a second time)
Goals: Changes from killing humans (including babies) to being a loving protector of humans, especially babies
Status: Alive (before the 150k-year time jump) and planning to settle into happy frontier domesticity with Baltar (babies a possibility)
Ellen Tigh
What kind of mother she is: created millions of "children" in lab; kind of tries to help them live with humans once she gets her memories back, but is still often an irresponsible alcoholic; apparently responsible for death of unborn Liam due to her jealous cattiness
Goals: save Cylon children from themselves, save Hera, break Tigh and Caprica Six up, get drunk and screw
Status: Alive and happily together with Tigh again (successfully defeated rival and possibly unintentionally killed rival's child to break that tie)
Head!Six
What kind of mother she is: Symbolic loving protector-mother (she starts telling Baltar about "their" tremendously important Cylon/human offspring on Kobol and guides events to fulfill that)
Goals: Get Cylons and humans to interbreed, get Hera to Earth to have babies
Status: Angel in the house
Kara Thrace
What kind of mother she is: Symbolic; not actually Kacey's mother, but important part of preparing for destiny is accepting idea of motherhood with Kacey as catalyst; spends second life dedicated to finding humanity (and Hera - tells Lee Hera may be their only hope) a home on Earth and disappears once goal is completed
Goals: Own goals shoved aside to focus on Special Destiny of guiding Hera (and Cylons and humans) to Earth; in essence, making world safe for motherhood
Status: Dead. Twice.
Maya
What kind of mother she is: Loving adoptive mother of Hera/Isis
Goals: have baby, teach schoolchildren with Roslin
Status: Dead
Mrs. King
What kind of mother she is: Grieving, motivated onscreen solely by son's concerns (both before and after his death)
Goals: Get help, then justice, for son
Status: Unknown
Sharon Agathon
What kind of mother she is: failed - she wanted a baby with Tyrol and didn't get one; has much bitterness over Hera not bonding with her despite her being identical to Hera's mother and tries to kill Hera; character arc resolves when she sacrifices herself to return Hera to rightful mother
Goals: marry Tyrol and have baby; kill or kidnap identical sister's baby when that fails
Status: Dead by her other self's hand
Did I miss anyone?
So... as far as I can tell, there's a pattern here: many mothers are abusive alcoholics or suicidal depressives who hurt their children and others' children alike (which may nevertheless be for the best sometimes, just to frak with your head); most mothers end up dead, quite possibly in the fridge (see: Cally Tyrol). (Fathers have better survival odds: see Adama, Balta, Helo, Tigh, Tyrol, Hot Dog...) The better mothers - and those with better odds of survival, though Maya shows it isn't guaranteed - place their children above every other concern in the universe, including the survival of the rest of their communities and their own lives. Frustrated motherhood is a terrible, destructive force, but when it goes right, it's so important that thousands of people will get roped into a destiny solely devoted to making sure one single person gets to be a mother someday. Because as the finale shows, that's what this whole show was about in the end: Hera growing up and having kids. All that "what is human?" and survival-in-the-face-of-tragedy stuff was just side trips on the way there.
This is an awful lot of pressure on motherhood in general and poor little Hera in particular. Remember when the show asked whether we deserved to survive as a species? I miss those days. Not necessarily because I want humanity wiped out (though at times during the show I was rooting for that ending), but because it feels like cheating to raise that question and then just take survival as a given, Of Course It's Good thing. And because it bothers me that so many Cylons just "naturally" would prefer to have babies instead of downloading without discussing the pros and cons first - it's a purely emotional reaction as far as I can tell. And because okay, you need mothers to have a next generation and all, but in a show so much about created family and friendship and co-workers being at least as important as biology, why did it come down to "it's all about the biological nuclear family, and good motherhood means saying 'frak everything but my kid'"? And I don't even know where to start with the idea that a fetus's father not loving the mother enough can actually kill the fetus...
But then, the show never pretended to be anything but a reflection of modern America and its values. So the historically and culturally specific 19th-21st century ideas about motherhood were bound to end up in there.