Atletico looked to be in with a great chance of reaching the Champions League quarter-finals after beating Juventus 2-0 at home in the first leg of their last-16 tie last month.
But a Cristiano Ronaldo hat-trick inspired Juve's second-leg turnaround, securing a 3-2 aggregate victory to dump Atletico out.
Simeone was criticised for a pragmatic approach in the second leg, as Atletico offered precious little in attack, but Morata believes flak is harsh on the coach, who has helped restore his own belief after a difficult period at Chelsea.
When asked if he is now happy at Atletico, Morata – who is away on Spain duty – told reporters: "Yes, especially at Atletico, but it would be more so if the last week had been better.
"We have been knocked out of the Champions League, but life goes on. Everyone knows what it means [to Simeone]. He is Atletico. A defeat in the Champions League or in the league is not [a reason] to criticise.
"I am where I wanted to be for a long time, I thank Simeone and the coaches for their confidence, because thanks to them I am finding my level.
"It's clear that I needed confidence [after leaving Chelsea], I came from bad times, but I do not have to consider the past."
Morata has scored three goals in eight total appearances for Atletico since joining from Chelsea in January.