Let $A$ be the event of picking the door hiding the car.
Let $B$ be the event of Monty revealing 98 goats.
Let $C$ be the condition that Monty cheats.
We seek $\mathsf P(A\mid B, C)$ and $\mathsf P(A\mid B,C^\complement)$, the probability that the contestant picked the door hiding the car when Monty reveals 98 goats under either condition (cheat, or not). By Bayes Rule, and the Law of Total Probability, these are:
$$\begin{split}\mathsf P(A\mid B, C) &~=~& \dfrac{\mathsf P(B\mid A, C)\mathsf P(A\mid C)}{\mathsf P(B\mid A, C)\mathsf P(A\mid C)+\mathsf P(B\mid A^\complement,C)\mathsf P(A^\complement\mid C)}\\\mathsf P(A\mid B, C^\complement) &~=~& \dfrac{\mathsf P(B\mid A, C^\complement)\mathsf P(A\mid C^\complement)}{\mathsf P(B\mid A, C^\complement)\mathsf P(A\mid C^\complement)+\mathsf P(B\mid A^\complement,C^\complement)\mathsf P(A^\complement\mid C^\complement)}\end{split}$$
Now, in either case, the probability for picking the door hiding the car is $1/100$. Further, if the contestant does so, only goats can be revealed.
$$\begin{split}\mathsf P(A\mid B, C) &~=~& \dfrac{1}{1+99\mathsf P(B\mid A^\complement,C)}\\\mathsf P(A\mid B, C^\complement) &~=~& \dfrac{1}{1+99\mathsf P(B\mid A^\complement,C^\complement)}\end{split}$$
Now, when Monty cheats he can certainly avoid revealing the car, so $\mathsf P(B\mid A^\complement, C)=1$. However, when Monty does not cheat, it is quite unlikely that he would miss the car when the contestant has not picked its door. $\mathsf P(B\mid A^\complement, C^\complement)=1/99$.
$$\begin{split}\mathsf P(A\mid B,C)&~=~&\dfrac{1}{100}\\\mathsf P(A\mid B, C^\complement) &~=~& \dfrac{1}{2}\end{split}$$
So if Monty is 'cheating' then you should switch doors, and if Monty is 'honest' then, eh, you may as well switch.
Now, is it rational to believe that if the car was in the remaining 99 doors, chances are that it'd have been revealed by now?
Yes. However, it is more likely that the car was among those 99 doors than that it was behind the 1 door the contestant picked. It balances out when Monty does not cheat.
There is a probability of $1/100$ that the contestant picked the car and Monty reveals $98$ of the $99$ goats behind the other doors. There is a probability of $(99/100)(1/99)$ that the contestant missed the car and that Monty did so too. So it is rational to believe it unlikely that either of these events would happen ($1/50$). However, when given that one from the two did happen, the (conditional)probability that the former happened is $1/2$.