According to Boxofficemojo, Paramount has three Transformers movies coming out for the next 3 consecutive summers 2017-2019. Assuming they each cost around $220m, and gross a minimum of $1bn each, as per Age of Extinction, Paramount's financial situation shouldn't become any wose in the next few years.
However, the Star Trek franchise is most definitely in murky waters.
Paramount has been the lowest performing of the major Hollywood studios for years now. Their revenue from 2015 was down $2.5 billion from 2014. Paramount is not in MGM kind of trouble but it does have a cash flow problem.
The only murky waters Star Trek movies are in are what type of movies Paramount should do going forward. Should they continue with the big blockbuster Trek movies trying to appeal to a large audience, or go back to the old model of lower budget story based Trek films that play to a niche market.