Is there a polite way to take the centre of the road without antagonizing motorists? The city I live in isn't especially well designed for cycling. 

There are some streets with parallel parking on the sides, and in this situation it's safer to ride in the middle of the lane as to force cars to pull right over to pass, (or wait), rather than trying to squeeze past on the same lane. 

However I get the feeling that this antagonises some motorists, even though it is the safest way to ride. 

Is there a way to ride safely, while minimising motorist antagonism?
In my experience, no. The problem is that however polite you try to be you're taking the lane so you're in their way.

My commute takes me over a narrow one-lane-each-way bridge that's a bit of a choke point, so it's busy. It's also a raised bridge, so sight lines are very poor. Since I ride it twice a day I've had the chance to experiment with some different approaches. Normally I ride during daylight, so I'm only considering that at the moment, but I have dynamo powered lights that are always on (they don't flash).

1: ride normally, take the lane
Result: most motorists are fine, perhaps 10% follow closer than I'd like (within 3m), occasionally one will (illegally) overtake, often failing to allow the 1m separation that I like, but since I have room I simply move away from them.

2: ride "politely" as close to the side of the road as I can
Result: 5-10% of motorists try to squeeze past me, often pulling back in before they have actually done so and forcing me to brake to avoid being hit. Some of them are aggressively close and these are the only times I've been abused.

3: take the lane, but turn my daylight-bright blinking lights on
Result: very few motorists follow too close, only one overtaking motorist and that was when there was clearly no oncoming traffic (still illegal, but relatively safe)

4: ride on the (narrow) footpath
Result: rather than being scared of misbehaving motorists, I'm now illegally terrorising pedestrians (of whom there are quite a few). I've only done this a couple of times, both because the road was packed with cars and I really didn't feel up to fighting for my place on the road. I don't feel good about it.

5: take the lane, lights on, helmet camera
Result: sore neck, as for (3) above.

I've basically stopped experimenting with this because the results are, in my opinion, conclusive. I turn my lights on when I leave the bike path a couple of hundred metres before the bridge (bright flashing lights on the shared path are, IMO, rude and unnecessary), or when I leave home (the bridge is ~1km from home). So I'm always using the flashing lights when I'm on the road.