Educational Travel to Cuba

I’m a senior in college with a service requirement to work in the homeland security field for a year after graduation. I just signed up for a three week study abroad program in Cuba for my major (political science) - will this definitively x out my chances of getting a clearance?

I obtained a Secret level clearance two years ago, and I have no other concerning factors.
Obviously I suspect more questions will be asked, but my trip is legal (sponsored by my accredited flagship university), I’ll be taking collegiate level classes while there to get credit, and obviously I have no plans to do anything against the US Government.

Will my trip lead to an automatic rejection, or just more questions?

If you are going as a part of a U.S. educational institute sponsored program with State Department approval then you are not doing anything illegal. Of course you will have to disclose this on future security clearance applications and most certainly will be queried about it, but as long as you are upfront and honest about it and you keep meticulous records of any foreign contacts then it will not be an issue.