The 29-year-old came off the bench with three minutes remaining in Bayern's 4-2 victory over Bayer Leverkusen in Saturday's DFB-Pokal final.
"The thing is, I always have hope. I'm actually always very positive about things," Flick told reporters following the Berlin triumph.
"I also know, of course, that when you're at a certain age and you've already played in the Spanish league with Barcelona and in the Bundesliga with Bayern Munich, you feel the need to experience another big league. That is quite normal and that is also human.
"I'm trying my best to make sure Thiago stays here and that you can convince him to stay. But that's one thing that time will show.
"We still have the Champions League ahead of us now and we have a lot of plans, also together with him."
Flick was also asked about Bayern's transfer plans after prising Germany international Leroy Sane from Manchester City.
Bayern have been linked to Leverkusen star Kai Havertz, who scored a late consolidation goal on Saturday, but Flick seemed to suggest the German giants won't be rushing back into the transfer market.
"We all know that of course the time with coronavirus has changed a lot," Flick added. "This means that many clubs, including FC Bayern Munich, can no longer spend money so easily. That's why we have to proceed cautiously.
"For now, Leroy Sane's commitment was important for the club and also for the team, which are taking the next step. Hasan Salihamidzic did a very good job of staying on the ball. I think a lot is developing and we have to see that we are a bit more broadly based."