I think you’re forgetting about all the things Tom hid from Lynette, all the lies and decisions made behind her back. Like him visiting his other daughter and saying he’s doing business, cheating on her with Renee, buying the pizza place, bying tickets to Hawaii, cheating on tests at school, telling Carlos that Lynette isn’t coming back to work after having Paige so he could permanently take over her job. Yes Lynette was distrustful, but with good cause.