Read newspapers, watch the national and local news channels, etc. This is where great ideas for thrillers originate.
I do believe actual experience helps. I do believe that the more a writer has gone through, the more a writer has done along the lines of action, violence, etc., the easier it will be to make a novel sound realistic, but as they say, if you can't use your own experience, you can always use someone else's.
But the main point, I think, is to be well-informed. Reading as many thrillers as possible is a must, but you can't draw on them for ideas. You read to learn structure, pace, characterization, etc. Ideas you should try to get elsewhere.
I would, however, also say that ideas are pretty much meaningless. It isn't the idea that makes a great novel, or where you get it, it's how well you write tthe novel, how well you draw the characters, how well you tell a story.
You say that the witness protection scheme has been used a million times, and you're right, so this should tell you something. It's been used so many times because it works, but it isn't used the same way each time, or with the same results. Few thrillers are about the witness protection program. Writers just use it as a trope, as a starting point, and there's nothing wrong with you using it, either.
You just have to add your own take on it, your own fresh, original story resulting from its use.
The main thing is to pick a character, all good thrillers begin with a good character, find any idea you like, jump right into the action, and keep the action coming. Take something out of the news, or just pick something. For instance, once you have a character, have him on vacation if Florida. He's sitting on the beach, idly digging in the sand while he watches the bikini clad women. His hand touches something in the sand, and he digs it out. It's a gold medallion with writing on both sides. It's in a language he doesn't know.
He takes it to an antique shop. Then someone breaks into his hotel room. Then someone tries to kill him. Just take it from there. Keep the action, the thrills coming. If you do tis, you can have romance, relationships, and whatever, as subplots. But keep teh action coming right from page one.
But the most important thing is to finish the novel. The way you learn to write any kind of novel is by writing them. You don;t learn by planning, by researching, by plotting, etc. You learn by starting a novel, and by finishing it. Then you write a second one. Like the first, you start it with a character and any idea, and then you finish it.