This depends on where you place the stretching point on the rope. The ant is moving with the rope if the rope is being held at its starting point. But if one assumes the midpoint of the rope along its length is the starting point, then the ant will actually be removed further from the endpoint of the rope in comparison to when the rope is not stretched.
If the rope is held in its middle, I think it's all a question of how long the rope can be extended until it snaps. Also don't forget ants have a certain lifetime. If one assumes the rope can be stretched indefinitely or not, one also has to assume how long an ant lives.
I can see where you are getting confused, I struggled to get my head around it for quite a while. The answer is, it doesn't matter where it is being stretched from (whether it be from one end or both ends), if the rope is stretched, then the ant will move along the rope with it.
Let's say for instance, that we put a mark with a pen on the rope 1m from the left hand end of the rope. If we then stretch the rope 1km, so that it doubles in length, does that mean that the mark is still 1m from the end, or now 2m from the end? If you suggest that it is still 1m from the end of the rope, then you have not stretched the rope, instead you have extended the length of the rope. Note, this is not the same as stretching it. If we then stretch the rope another 1km, not extend, then the mark will now be 3m from the left hand end.
If you don't believe me, try this with an elastic band and two screws. Take a 5cm diameter elastic band and mark it three times, two directly opposite each other, and another mark 1cm anti-clockwise from one of the marks (preferably facing towards you). Screw the two screws into a piece of wood 5cm apart, lining up the marks so they are opposite each other on the screws, and measure the mark on the elastic band. You should find that it will be 1cm from the left hand screw. Now take the right hand screw out and move it another 5cm to the right (so now it is 10cm from the one on the left). Align the marks, and you will find the third mark is now 2cm from the one on the left. Note, you haven't extended the original length of the elastic band, merely increased the distance covered by the material. As you increase the material, so you increase the surface, and it's this that makes the ant move along the rope faster than the 1cm/s it can travel under it's own power.
So, how does this answer your points? While it is true that the endpoint is further away from the ant with each passing second in terms of distance, the percentage of the total distance actually decreases as it moving along the rope at 1cm/s plus a fraction of the total movement of the rope. When the ant reaches the relative midway point of the rope, it will actually start to get the end of the rope faster and faster (relatively speaking) than it was before it reached the midway point.
As for your second point, this experiment is a hypothetical one, requiring an elastic rope that will never break, and an ant that will last eternity. As for how long it would take, I would take a guess at around a couple of hundred million years.