Shane gets this too, for those who think he crossed a Moral Event Horizon when he "outed" Karma and Amy as lesbians in front of their classmates without their consent.
Reagan got a lot of hate after breaking up with Amy because she wouldn't commit to being a lesbian rather than maybe still have feelings for guys...but there's still a small chunk of the fandom that prefers Reamy over Karmy. A few of these are the fans that were firmly on the side of wanting Amy to be fully lesbian, making Reagan a bit of an Audience Surrogate for them.
Broken Base: The first season finale when Liam and Amy have sex. Some thought it drudged back up a terrible lesbian cliche, others thought as Amy had not actually identified herself as a lesbian, the argument could still be made that she's figuring things out or that it was simply an act of revenge against Karma.
Draco in Leather Pants: Amy is obviously not the bad guy of the show, but plenty of fans praise her while in the meantime criticizing Karma despite the fact the two of them are equally not perfect.
Ensemble Dark Horse: Of the main five, Lauren is the one most people will want to protect at all costs. Of the recurring cast, Principal Penelope is quite beloved, mostly due to the fact that she's definitely a Karmy shipper (despite apparently not liking Karma all that much since she revealed she's not a lesbian).
Fan-Preferred Couple: The show seems to be trying to sell Karma/Liam as much as Karma/Amy. Pretty much no one is rooting for the first ship. So far every single fanfic is Karmy and Katie Stevens and Rita Volk seem to ship it themselves. Those that do sometimes pair Liam with Shane. The writers were moving Liam away from Karma...and possibly on to Lauren...when the series was cancelled.
Fridge Brilliance: Bruce seems much more accepting of Amy being gay than Farrah. It makes sense in Season 2 when it's revealed that Lauren is intersexed.
"Funny Aneurysm" Moment: Meanwhile, Lauren's secret (that she's intersexed) makes the tampon up her boyfriend Tommy's nose to stop the bleeding from a fight in "Three to Tango" a bit more complicated...For starters, did he get it from Lauren?
Ho Yay: Liam and Shane experience a few instances of it, such as Shane leaning his head on Liam's shoulder.
Hollywood Homely: Dialogue suggests that Amy is supposed to be plain and unconcerned with her appearance; everyone (including Amy herself) automatically peg her as "the butch one" in her relationship with Karma.
Unconcerned with her appearance, yes. Plain, no. When she goes to the lesbian bar, all the girls she flirts with seem very receptive to her advances - until she screws it up by being obnoxious or running away.
Jerkass Woobie: Yes, Lauren isn't the nicest of persons, but she simply hasn't caught many breaks and she's right in that at another school, she'd be a queen. She acts out, yes, but people forget that she's been uprooted from her home, she has no real friends, there's no one at her high school that she can connect with (save Shane, and she's pointed out that neither of them are very nice people). Still, she's amazing at helping with Farrah's wedding, she empathizes with Amy after their mutual breakups, she manages to maintain a friendship with Pablo (who she actually attempts to protect from Shane's dating style), and she never told their parents about Amy & Karma's entire scheme. (Yes, she tried to bust them at school, but it wasn't personal.) On top of everything, she was born intersexed. Basically, the only person she consistently has the upper hand on is Principal Penelope.
Les Yay: This leads to Karma and Amy being mistaken for lesbians in the first place.
No Such Thing as Bad Publicity: The criticism from LGBT websites is one of the main reasons people know about it. Many of the LGBTs who watched the show to see what the fuss was about ended up falling in love with the show and Amy in particular.
Ron the Death Eater: There's a fair portion of the fandom who villainize Karma for practically everything that she does.
Karma was moving into this territory for a sizable part of the fanbase in season 2, as possible Flanderization has made her even more self-centered and melodromatic than before, and some think she's intentionally undermining Amy's relationship with Reagan because she's no longer the sole focal point of Amy's world. On the other hand, some would justify Amy's increasing coldness toward Karma after getting together with Reagan and the whole thing with Liam is partial justification for Karma's modest exaggerations in character. Gained more sympathy towards the end of Season 2 after Amy and Liam's secret was revealed.
Reagan became a big one after her and Amy's breakup in season 2B, mainly for her reluctance to keep dating Amy for not identifying as a lesbian and a portion of the fanbase's general anger that it was reinforcing a very ugly stereotype about the LGBTQ community.
Sophomore Slump: Definitely arguable, but there has been some vocal dislike about the second season's direction from the fandom, especially the turn from the sharper and more satirical style of the first season to rather over-the-top, melodramatic plotting, the perceived Flanderization (see Shane) of its main characters or subjugating them into a Straw Villain (see Reagan), and the drawn-out baiting of the main Karma/Amy ship. Ratings have also declined rather steeply.
Ship-to-Ship Combat: Although dominated by Karmy, there are those that hold out hope for Kiam (and even a few Lamy (Liam and Amy) shippers after the first season finale.)
Karmy now has a new enemy in Reamy, due to Amy getting a girlfriend of her own in season 2.
It does seem odd he wouldn't be suspicious of Karma being straight or at the least bisexual when she spends a lot of energy either explicitly flirting or even trying to sleep with him... Liam definitely doesn't seem to be the sharpest tool in the shed. However, even Shane, who's gay, seems to forget (or in the case of men, deny) that bisexuals even exist.