Yes, NEET is more difficult than JEE Main, because of the limited seats. The number of seats in medical institutes is lower compared to engineering colleges, so even though the difficulty level of the questions in NEET is less than in JEE Main, it is more competitive. If you rank lower in JEE Main, you will have the option to opt for private colleges. While most students appearing in NEET, target Govt. medical colleges. Since private medical colleges cost a fortune.
If we compare NEET and JEE Main, in terms of difficulty then the latter is more difficult. As most of the questions come from a moderate level. However, when compared based on the competitive level, NEET is definitely more difficult. The reason is the limited number of seats available in Govt. medical colleges.
Both examinations have their difficulty. But considering the factors, NEET is more difficult than JEE Main.