These two phenomena/observations are inherently different.
Consider a high-speed rocket entering the Earth's atmosphere. So, atmosphere's particles will hit the rocket with a high speed and this leads to converting the rocket's kinetic energy into heat, mostly through compression of air and less by friction with the air 1. As a result, the rocket begins to heat up. This heating continues constantly because the Earth's gravity is constantly applying force to the rocket and increasing its vertical velocity. As a result, the rocket begins to burn. See more details in WikiPedia.
When you ride a motorcycle (at low speeds), most of the heat energy of your motorcycle's engine is spent on warming up your engine and its temperature increases more and more than the outside (environment) temperature. When you start moving, more cool air particles hit your engine and the heat transfer rate from the engine to the environment increases. So, your engine starts to get cooler. In this phenomenon, the relative velocity of air particles with respect to your engine is much much lower than the previous phenomenon (i.e., the rocket entering the atmosphere), therefore it cannot cause a great amount of heat through air resistance (compression of air as well as friction with air).
In conclusion, in the first phenomenon at high speeds, the rocket absorbs a huge amount of heat while, in the second phenomenon at low speeds, the motorcycle loses heat.
1 To make it more clear consider a cylinder that contains a specific gas. When you compress the gas by a piston, the pressure increases and, as a result, the gas’ temperature rises. This is an example of adiabatic process. In a thermodynamic adiabatic process, no heat is transferred between the system (here air or any gas) and its surroundings. In this example, the thermodynamic work is done by you (through compressing the gas). In the atmosphere reentry of a rocket, the rocket compresses the air in front of it (so work is done on the air by rocket). Because of air compression, the volume of air is decreased suddenly and thus the air’s temperature rises significantly. Subsequently, the rocket heats up due to direct contact with the hot air in front of it. So, rocket loses its kinetic energy, the air’s temperature is increased, and finally the rocket absorbs the heat from the hot air. This means the kinetic energy of rocket is converted to heat.