A new Neato or Roomba has to have several full runs to adapt to the power capacity of the batteries, because the robot you purchased has been travelled from the factory and stored in stock for a few months without re-charging.
The charging should take longer than 45 minutes to recharge a flat battery. If after the run in cycles the robot only has less than 45 minutes of run time on a hard floor and 45 minutes of charging then the batteries might need to be replaced.
Also, the power capacity of the batteries could temporary degrade when the robot has been stored for a long time (more than a few weeks) without recharging. If it happened, in addition to several runs, you may also need to reset the battery charging system. If you have a Neato, you should go to the menu "Support | New Battery". For the Roomba owners, you should turn the robot on, then press both buttons above and below the "Clean" ("Dock" and "Spot") at the same time for about 8 seconds. For both robots, it is recommended to connect the charger directly to the robot and wait until it indicates full charge. It might take up to 16 hours, please refer to your User Manual.
Please also notice that dirty brushes and filters negatively affects the run time. Keeping the robot clean is an easy way to extend both battery run time and their life term.
You should always remove the batteries for long-term storage, which is more than a few weeks. Store the batteries in a cool and dry place. Batteries must be stored only after being fully charged. When you want to use your robot again, insert the batteries and fully charge it.
During the battery life time they are gradually loosing the capacity, which is normal for batteries of any type. Thus, after 2-3 years you should usually expect the robot to have about 1/2 of initial running time (may vary depending on usage and storage). At this point you might like to replace the batteries.
The guidelines listed above are the basic rules that could be applied to any battery operated equipment.
If you are not happy with the battery runtime, then you might like to replace the batteries with new ones:
Roomba Replacement Batteries
Neato Replacement Batteries
Roomba Battery Maintenance Tips
Robot reviews: "Battery run time between charges too short" thread