HTC was probably a target due to their relationship with Google and strong support of Android. HTC relies on Android for the bulk of their handsets these days so they might be more likely to reach a deal with Apple. Moto only has a couple Android handsets and likely has their own patent war chest to fight back with. Palm isn't selling enough handsets to be a good target at this point. They'll probably fall into line if HTC loses. (or they'll be out of business)
For example, Engadget ran an analysis on Palm vs. Apple a while ago. They found that both companies infringed heavily on each other's patents, for things from list scrolling to three-way calling. Starting that particular food-fight would probably end badly for both companies.
HTC is a much softer target. HTC is relatively new in the business, with a smaller patent portfolio. They're also a foreign corporation, which may give Apple some home advantage in the courtroom.
At its core, this is all about Google. Every single Google developer phone has been HTC, as well as the G1 and Nexus One. If Apple prevails, that would be a pretty big blow to Google just as Android is beginning to spread its wings.
Not all of the complaints are cellphone specific. Some of the patents in the filings are from the NeXT days, long before HTC was around.
Now, both parties are "all-in", and by attacking now, Apple can hurt both companies badly, and put the competition back 2-3 years.
Nobody sues if they can avoid it. Lawsuits are extremely expensive, and companies will exhaust all other options first. The lawsuit means Apple demanded more than HTC was willing to pay, and decided they would fair better in court.
Also, "iPhone knockoffs" doesn't necessarily mean patent infringements. Without doing in-depth research into the specific claims infringed, you can't say for sure whether any infringement took place.
Patents and patent law are incredibly complicated. There is no simple answer to _why_.
I'm not saying Apple should have won or that that case isn't in some ways relevant--only that it wasn't certain that they would lose.