The fork rake, tire size, and head angle determines the trail. The trail reflects how stable the bike will or will not be and at what speeds.

A link to a calculator is posted below. IMO, people tend to greatly overstate the effect of minor changes (40mm vs. 43mm) in fork rake.

http://www.kreuzotter.de/english/elenk.htm

So is it the smaller the rake the quicker the handling vs the larger the rake the better the handling at higher speeds?

I quess since my bike came with a 43mm fork I should probably stick with a fork with the same fork rake.

Bike makers tend to design frames (or choose forks for a frame) with a particular fork rake in mind. Changing the rake can have ill effects on how a bike handles that maybe the manufacturer did not plan for given the rake thay had in mind when they designed the bike. It's just like how using a forward seatpost (and drastically changing the effective seat angle of the frame) can have negative effects on the ride quality and handling of some frames. So if you have a bike that was designed with ride quality and handling in mind, and you want retain as much of those qualities as possible, I'd recommend using the same rake in any new fork you may buy for the frame.

As for how rake affects trail, it's a little counter intuitive. A smaller rake increases trail while a larger rake decreases it. So in general terms increasing the rake often makes handling a bit "twitchier".

OK, I'll add an edit. These sorts of changes don't only mean the bike becomes more or less twitchy. It could also introduce some strange behavior like speed wobble (or death wobble) at high speeds. You really don't know until you try. You do know though that these things have likely been addressed in the factory setups for bikes from quality manufacturers.

There are several other factors than rake. Too little rake can make the bike nervous, too much can make it ponderous and hard to steer. There are other things like fork stack (runs from the centre of front wheel to the intersection of head tube centre line and bottom of the head set). Then you have to take into consideration the stack height of the headset. Ves taught me something I did not know. He's one hell of a smart guy.

You really have to watch it when messing with the fork on your bike. I am now convinced that possibly a person who knows frame building (who is smarter than I, for certain) is the only one who can help make a decision for your new fork. They can help decipher some of the harder elements of making the correct choice on your fork.

So is it safe to say if my bike came with a fork with an 43mm rake and I'm looking to purchase a more aero fork it should also have a 43mm rake.

"should also have a 43mm rake"

Depends. :-) Bunnyman's point about stack height is that if the new fork winds up lowering (for example) the head tube a bit, that increases head tube angle, which affects trail, which affects handling -- so rake should be adjusted to compensate in such a case. What you want is a fork that holds the wheel in the same position relative to the head tube, which means two dimensions need to be correct: the rake, and the dimension along the head tube axis from the rake measurement point (ie, opposite the dropout) to whatever your reference point is that corresponds to a fixed point on the head tube. The latter dimension is not as critical, but can be significant.