I'd love to help with your question - although I will say at the outset that I don't think I'll be able to give you an exact answer! However, I'd be happy to explain the situation a little bit and give you my opinion.
Basically, if you think about it, babies only have a few ways to tell us anything that's on their mind... and crying is first and foremost among those. When your son is 3, he'll have no problem telling you that he's hungry, or that his tummy hurts, or that he had a bad dream. But a baby will describe all three of those things in exactly the same way: by crying!
The fact that your son calmed down after 5 minutes and has otherwise been well is very reassuring. If he had a serious problem - for example, pain that wasn't going away - he wouldn't do that.
My advice to you is probably to do what you just did. When your baby cries, see if you can figure out what he's trying to tell you. It may be that he's hungry, or that he wants to be held, or that he needs to pass gas or wants a diaper change or to be burped. So just like you did, you work through that kind of checklist and see if you can find a need that's not met. Sometimes you will; sometimes you won't. But like I said, if your little guy quits crying, odds are that you've addressed whatever he wanted you to address (even if you didn't know that you did), or that whatever he was upset about before has passed.
If you ever have a time when he won't stop crying - particularly if he's doing other things that concern you like not feeding or not acting like himself - then it's time to call your pediatrician and figure out what to do next.
I hope that this information is helpful to you. If I've answered your original question, please take a moment to rate the quality of my response - your feedback does matter! And if you have any more questions - now or in the future - please do not hesitate to ask.
Best wishes to you and your son...