Hello Sijo,

JEE main is not one and only entrance exam to get seat in Aeronautical Engineering.Ofcourse if you appear for JEE main and JEE advanced and  qualify, you will get a seat in prestigious institutes like IITs/NITs/IIITs.Apart from JEE there are other private institutes or deemed universities who conduct their own entrance exam for various B.tech courses including aeronautical engineering.Also JEE main score in accepted by many colleges.You can choose any way to get in Aeronautical Engineering depending upon your choice of college.

I hope this is helpful to you.