"Hate" is probably a strong word, as Top said - although I've probably used it when talking about Lindsay, especially when I'm annoyed.
Mostly, I just don't like her. She's never been a character I connected to. I don't like that from her first season onward she took time away from other characters who I think are more deserving of screentime (specifically Hawkes - if they acknowledged that Hawkes got the shaft in S2 because they needed to introduce Lindsay, it boggles my mind that they never bothered to make it up to him in later seasons). The character started out with potential, but by season 5 she seems to have less going for her than she started with.
Anna having kids doesn't bother me, honestly - it's her right, and I wouldn't want someone to say I shouldn't have kids if I was in that position. (Not that I think anybody here is saying that, I'm just pointing out my own feelings.) My problem is with how they've dealt with the pregnancies on the show itself. The choice to write in the pregnancy this season seems to have put the final nail in the coffin, essentially reducing Lindsay to a glorified love interest - and she's been teetering on the brink of that classification for a while. Even as we've watched the character go through her very first pregnancy, we've seen little more than 'Yay, I'm excited to have a baby' from her. It's like she's just carrying Danny's child and there's nothing the character can contribute to the storyline.
I don't think Anna is the worst actress on TV, but I think she stands out compared to the other people on the show because they're all just so talented. However, I think if the writing was tailored to her individual strengths, I might have developed at least some small amount of fondness for her in the four seasons she's been on the show. As of right now, I can't see it happening, and a lot of that is on the writers' shoulders.
Also, I think her demonstrations are annoying and not at all cute, and as others have said, I don't like that she seems to get handled with kid gloves.
Aiden is long since dead and gone - I feel like hating Lindsay because of Aiden would be ridiculous at this point. My problem wasn't that she replaced a character I liked - the problem was that she couldn't fill her shoes. Aiden was feisty and really felt like she belonged in NYC, not to mention that she was flirtatious without strings attached (if that makes sense). Lindsay, on the other hand, has been inconsistent, and they have always emphasized her being From Montana without ever really delving into the interesting possibilities her being an outsider would provide - plus, I think it's obvious when flirtation is planned rather than finding its way into the show organically. Sometimes it works and sometimes it doesn't - and in this case, I don't think it works. (And it's continued to not work all the way to the altar - or the clerk's office, anyway.)