Are the real life spies as tough and well-trained in combat as shown in the movies, like James Bond, Jason Bourne, etc.?

In most cases, they are not, unless someone is tough in a natural way. Well trained -there could be a possibility. However, most of their training happens to be on technicalities, survival, using technical gadgets, coding & decoding, communication techniques, language, culture, adaptation, building intimacy, etc. They are extensively briefed on how to act without raising any suspicion, or on not getting caught. An extraordinary tough-looking muscular agent would draw unnecessary attention which would act as a hindrance or could alert the opponent and the security agency. Anyone gets suspicious if a few burly-looking guys close in. So even though the job demands, the agents have to compromise on this aspect. Recruiters would always prefer an average-looking unsuspecting person.

The success of a secret agent lies mostly in being unseemingly special. They have to avoid looking special, or extraordinary in any manner to draw attention. So you wouldn’t find an agent pumping iron unless he is mixing up with a crowd where not pumping iron would be unnatural. So you would find an agent to be absolutely commoner without drawing any attention, without raising any suspicion. Even in the cases where they build up intimacy deliberately - they have to make it look absolutely natural and keep it away from public glare.

The secret agents are primarily required to undertake three types of functions.

1. Intelligence gathering and transmission- For this function physical toughness or combat martial arts training is not an essential condition. Rather an agent on the weaker side will always rely more on his intelligence and avoid confrontation rather than relying on his combat ability.
2. Information Dissemination- This is by far the most important function for which agents are extensively used. Here they have to mix up with the target group or individuals in an unseemly manner in various capacities to influence them. Here also physical toughness is not an essential condition
3. The third major function is Sabotage - Agents are required to undertake sabotage activity, assassination as well as character assassination activities.. But here also their technical skill is more important than their combat skill. As already mentioned a burly-looking guy would immediately send an alert or alarm bell to the target and to the security agencies. Any display of combat skill will only send a higher level of alert and the risk of disclosing their identity and endangering their life.

So even in the face of getting apprehended, they have to act as if they are normal individual especially when chances of escape are low or they are being watched. No country takes responsibility if its agents get caught in a foreign land. So it is better to get caught as a normal individual rather than as a spy as the punishments are lighter. Secondly, your country could come to your defense without getting implicated. So in real life, you would not know if you are living in close proximity to a spy. In modern-day espionage, a major share of intelligence gathering and information dissemination happens through system hacking. So a spy is required to be a technical expert in IT & networking rather than being a combat skill expert for kicking around.